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1.
N transfer in three-species grass-clover mixtures with chicory,ribwort plantain or caraway 总被引:1,自引:0,他引:1
Nawa Raj Dhamala Jim Rasmussen Georg Carlsson Karen Søegaard Jørgen Eriksen 《Plant and Soil》2017,413(1-2):217-230
Background and aims
There is substantial evidence that legume-derived Nitrogen (N) is transferred to neighboring non-legumes in grassland mixtures. However, there is sparse information about how deep rooted non-legume forage herbs (forbs) influence N transfer in multi-species grasslands.Methodology
Red clover (Trifolium pretense L.) was grown together with perennial ryegrass (Lolium perenne L.) and one of three forb species: chicory (Cichorium intybus L.), ribwort plantain (Plantago lanceolata L.) or caraway (Carum carvi L.) in a field experiment. During the first year after the establishment, red clover leaves were labeled with 15N-urea to determine the N transfer from red clover to companion ryegrass and forbs.Results
On an annual basis, up to 15 % of red clover N was transferred to the companion ryegrass and forbs, but predominantly to the grass. The forb species did not differ in their ability to take up clover N, but biomass production and soil N acquisition was higher in chicory and plantain than in caraway.Conclusions
Grass relied to a great extent on clover N, whereas forbs relied on soil N. Soil 15N-enrichment indicated that N transfer occurred in the upper soil layers and that a dependence on clover-derived N did not necessarily give grass a growth advantage.2.
Timothy I. McLaren Michael J. McLaughlin Therese M. McBeath Richard J. Simpson Ronald J. Smernik Christopher N. Guppy Alan E. Richardson 《Plant and Soil》2016,401(1-2):23-38
Background and aims
Single superphosphate (SSP) is a major source of phosphorus (P) used in grazing systems to improve pasture production. The aim of this experiment was to determine the fate of fertiliser P in clover pastures under field conditions.Methods
A procedure was developed to radiolabel SSP granules with a 33P radiotracer, which was then applied to the soil surface (equivalent to ~12 kg P ha?1) of a clover pasture. Recovery of fertiliser P was determined in clover shoots, fertiliser granules and soil fractions (surface layer: 0–4 cm and sub-surface layer: 4–8 cm).Results
The P diffusion patterns of the 33P-labelled SSP granules were not significantly different to those of commercial SSP granules (P?>?0.05). Recovery of fertiliser P in clover shoots was 30–35 %. A considerable proportion of the fertiliser P (~28 %) was recovered in the surface soil layer and was largely inorganic P.Conclusions
Recovery of fertiliser P by clover plants was up to 35 % in the year of application. Much of the fertiliser P in soil fractions was inorganic P, which highlights the importance of inorganic P forms and dynamics in soils under clover pasture on a single season timeframe at these sites.3.
Shiwei Zhang Qiding Zhong Daobing Wang Zhanbin Huang Guohui Li 《Biotechnology letters》2017,39(12):1853-1857
Objectives
To determine the origin of 15N-labeled phenylalanine in microbial metabolic flux analysis using 15N as a tracer, a method for measuring phenylalanine δ15N using HPLC coupled with elemental analysis-isotope ratio mass spectrometry (EA-IRMS) was developed.Results
The original source of the 15N-labeled phenylalanine was determined using this new method that consists of three steps: optimization of the HPLC conditions, evaluation of the isotope fractionation effects, and evaluation of the effect of pre-processing on the phenylalanine nitrogen stable isotope. In addition, the use of a 15N-labeled inorganic nitrogen source, rather than 15N-labeled amino acids, was explored using this method.Conclusions
The method described here can also be applied to the analysis of metabolic flux.4.
Elif Erdem Ibrahim Inan Harbiyeli Hazal Boral Macit Ilkit Meltem Yagmur Reha Ersoz 《Mycopathologia》2018,183(3):521-527
Purpose
To evaluate the efficiency of corneal collagen cross-linking (CXL) in addition to topical voriconazole in cases with mycotic keratitis.Design
Retrospective case series in a tertiary university hospital.Participants
CXL was performed on 13 patients with mycotic keratitis who presented poor or no response to topical voriconazole treatment.Methods
The clinical features, symptoms, treatment results and complications were recorded retrospectively. The corneal infection was graded according to the depth of infection into the stroma (from grade 1 to grade 3). The visual analogue scale was used to calculate the pain score before and 2 days after surgery.Main Outcome Measures
Grade of the corneal infection.Results
Mean age of 13 patients (6 female and 7 male) was 42.4 ± 17.7 years (20–74 years). Fungus was demonstrated in culture (eight patients) or cytological examination (five patients). Seven of the 13 patients (54%) were healed with topical voriconazole and CXL adjuvant treatment in 26 ± 10 days (15–40 days). The remaining six patients did not respond to CXL treatment; they initially presented with higher grade ulcers. Pre- and post-operative pain score values were 8 ± 0.8 and 3.5 ± 1, respectively (p < 0.05).Conclusions
The current study suggests that adjunctive CXL treatment is effective in patients with small and superficial mycotic ulcers. These observations require further research by large randomized clinical trials.5.
Shimpei Oikawa Hitomi Ehara Mika Koyama Tadaki Hirose Kouki Hikosaka Charles P. Chen Hirofumi Nakamura Hidemitsu Sakai Takeshi Tokida Yasuhiro Usui Toshihiro Hasegawa 《Plant and Soil》2017,413(1-2):231-242
Background and Aims
The effects of Sb(V), alone or combined with Se, on the growth and root development of plants are unknown. The aim of this study is to investigate the interaction between selenite and different forms of Sb and the effects on their uptake in rice and on rice root morphology.Methods
A hydroponic experiment was conducted that contained fourteen treatments. The treatment levels for Se were 0.5 and 1 mg L?1, and the treatment levels for Sb(III) and Sb(V) were 5 and 15 mg L?1.Results
Sb(V) alone significantly reduced the surface area, mean diameter and volume of the roots, whereas Sb(III) alone reduced the values of most parameters of root morphology. The addition of 1 mg L?1 Se significantly enhanced the surface area, number of medium roots, and Sb concentration in the roots subjected to 15 mg L?1 Sb(V), but it decreased the number of root forks, the number and proportion of fine roots, and the shoot Sb concentration under exposure to 15 mg L?1 Sb(III). When the plants were subjected to 1 mg L?1 Se, the addition of 15 mg L?1 Sb(III) markedly reduced the shoot and root Se concentrations and the number of root tips, root forks, and fine roots and increased the mean root diameter. However, the addition of Sb(V) did not significantly affect the root and shoot Se concentrations but significantly decreased the number of root forks and fine roots and increased the proportion of medium roots.Conclusions
Se and Sb(III) showed antagonistic effects on uptake in the shoots, but not in the roots, of paddy rice. A range of Se concentrations could stimulate the uptake of Sb in both the shoots and roots of paddy rice exposed to Sb(V).6.
Aims
The mechanisms underlying magnesium (Mg) uptake by plant roots remain to be fully elucidated. In particular, there is little information about the effects of Mg deficiency on Mg uptake activity. A Mg uptake kinetic study is essential for better understanding the Mg uptake system.Methods
We performed a Mg uptake tracer experiment in rice plants using 28?Mg.Results
Mg uptake was mediated by high- and low-affinity transport systems. The K m value of the high-affinity transport system was approximately 70 μM under Mg-deficient conditions. The Mg uptake activity was promoted by Mg deficiency, which in turn fell to the basal level after 5- min of Mg resupply. The induced uptake rate was inhibited by ionophore treatment, suggesting that an energy-dependent uptake system is enhanced by Mg deficiency.Conclusions
The Mg uptake changes rapidly with Mg conditions in rice, as revealed by a 28?Mg tracer experiment. This technique is expected to be applicable for Mg uptake analyses, particularly in mutants or other lines.7.
Tim R. Moore Muriel Abraham Margaret Kalácska Meaghan T. Murphy Catherine Potvin 《Plant and Soil》2018,425(1-2):133-143
Background and aims
We examined changes in soil organic matter arising from conversion of a 45-year old pasture to a 10 yr. old native tree plantation in Panamá, to evaluate the effect of monoculture and mixtures.Methods
We intensively sampled the soil 0–10 cm depth in the pasture in 2001 and in 22 plantation plots in 2011, ranging from 5 monocultures to 3- and 6-species treatments; samples were also taken from an undisturbed forest site. Soil analyses included organic carbon (SOC) and δ13C.Results
Conversion of the pasture to tree plantation resulted in an overall loss of SOC of 0.6 kg m?2 (18%) in the top 10 cm, but neither tree species nor diversity had a significant effect. End-member δ13C values suggested that the contribution of C3 plants to SOC was increased from 26% in the pasture to 55% after 10 years of plantation and SOC turnover times were calculated to be 21–36 yr.Conclusions
The magnitude of the loss in soil SOC is smaller than the increases in tree biomass (~3 kg C m?2) and litter (~0.3 kg C m?2) in the plantation, but still a significant part of the ecosystem C balance.8.
Aims
The role of different soil types for beech productivity and drought sensitivity is unknown. The aim of this experimental study was to compare mycorrhizal diversity between acid sandy and calcareous soils and to investigate how this diversity affects tree performance, nitrogen uptake and use efficiency (NUE).Methods
Beech trees were germinated and grown in five different soil types (pH 3.8 to 6.7). One-and-a-half-year-old plants were exposed for 6 weeks to sufficient or low soil humidity. Tree biomass, root tip mycorrhizal colonization and community structure, root tip mortality, leaf area, photosynthesis, nitrogen concentrations, NUE and short-term 15N uptake from glutamine were determined.Results
Soil type did not affect photosynthesis or biomass formation, with one exception in calcareous soil, where root mortality was higher than in the other soil types. Beech in acid soils showed lower mycorrhizal colonization, higher nitrogen tissue concentrations, and lower NUE than those in calcareous soils. Drought had no effect on nitrogen concentrations or NUE but caused reductions in mycorrhizal colonization. Mycorrhizal species richness correlated with nitrogen uptake and NUE. Nitrogen uptake was more sensitive to drought in calcareous soils than in acid soils.Conclusions
Beech may be more drought-susceptible on calcareous sites because of stronger decrease of organic nitrogen uptake than on acid soils.9.
Andres Gil David Siegel Silke Bonsing-Vedelaar Hjalmar Permentier Dirk-Jan Reijngoud Frank Dekker Rainer Bischoff 《Metabolomics : Official journal of the Metabolomic Society》2017,13(1):1
Introduction
Boiling ethanol extraction is a frequently used method for metabolomics studies of biological samples. However, the stability of several central carbon metabolites, including nucleotide triphosphates, and the influence of the cellular matrix on their degradation have not been addressed.Objectives
To study how a complex cellular matrix extracted from yeast (Saccharomyces cerevisiae) may affect the degradation profiles of nucleotide triphosphates extracted under boiling ethanol conditions.Methods
We present a double-labelling LC–MS approach with a 13C-labeled yeast cellular extract as complex surrogate matrix, and 13C15N-labeled nucleotides as internal standards, to study the effect of the yeast matrix on the degradation of nucleotide triphosphates.Results
While nucleotide triphosphates were degraded to the corresponding diphosphates in pure solutions, degradation was prevented in the presence of the yeast matrix under typical boiling ethanol extraction conditions.Conclusions
Extraction of biological samples under boiling ethanol extraction conditions that rapidly inactivate enzyme activity are suitable for labile central energy metabolites such as nucleotide triphosphates due to the stabilizing effect of the yeast matrix. The basis of this phenomenon requires further study.Graphical abstract
10.
Qing-Yi Lu Xuemei Zhang Jieping Yang Vay-Liang W. Go Wai-Nang Lee 《Metabolomics : Official journal of the Metabolomic Society》2017,13(4):39
Introduction
Loquat leaf extract (LLE) is a mixture rich in terpenoids, and has broad biological activities including the inhibition of cancer cell growth. The exact metabolic mechanism of this growth inhibiting effect is not known.Objectives
We investigated the cellular metabolic effect of LLE, and ursolic acid (UA) on pancreatic cancer cells using a 13C carbon tracing technology.Methods
MIA PaCa-2 cells were cultured in medium containing [1, 2 13C2]-glucose in the presence of either LLE (50 µg/ml), UA (50 µM), or metformin (1 mM). The mass isotopomer distribution of glucose, lactate, ribose, glutamate and palmitate in medium was determined. Based on the mass isotopomer distribution in metabolites we were able to determine individual 13C enrichment (∑M?×?n) and the minimum fraction of new synthesis?(1-M0) in each metabolite. Several flux ratios of energy metabolic pathways were calculated from the mass isotopomer ratios of these metabolites.Results
We found that tumor viability was suppressed by LLE and UA in a dose dependent manner, and the tumor-inhibiting effect was associated with the changes in oxidative/non-oxidative pentose (Ox/Non-ox) and pyruvate dehydrogenase/isocitrate dehydrogenase (PDH/ICDH) flux ratios resulting in decreased new syntheses of ribose and fatty acids.Conclusion
Metabolic homeostasis (balance of fluxes) in cancer cells is maintained through the regulation of metabolic fluxes by oncogenes and tumor-suppressor genes. Treatment of MIA PaCa-2 cells by LLE, UA and metformin likely altered key metabolic flux ratios affecting metabolic homeostasis required for energy and macromolecular production in tumor growth.11.
Baolong Wang Xin Wang Chris Wayne Xiangxiang Wang Lei Han Li Ye Qun Zhao Guixiang Jiang Meiqing Feng 《Biotechnology letters》2016,38(5):801-807
Objective
To produce a therapeutic protein (endostatin) by fusion with two fragments of the carboxyl-terminal peptide (CTP) of the human chorionic gonadotropin β-subunit in Pichia pastoris.Results
Two CTP sequences were fused to the C-terminal of human endostatin, and the fusion protein (endo-CTP) was expressed by P. pastoris. Endo-CTP inhibited proliferation of endothelial cells with an IC50 of 7 μg ml?1, and 30 % of cells were annexin V-positive after treatment with 20 μg endo-CTP ml?1 for 48 h. Migration of endothelial cells was inhibited by endo-CTP in a concentration-dependent manner. The half-life of endo-CTP in Sprague–Dawley rats was much longer than that of its commercial counterpart (Endostar).Conclusion
A long-acting endostatin can be produced using CTP technology.12.
Improving N management through intercropping alleviates the inhibitory effect of mineral N on nodulation in pea 总被引:7,自引:0,他引:7
Background and aims
Symbiotic N2 fixation is essential in the development of sustainable agriculture, but the nodulation of legumes is usually inhibited by N fertilization. Here, the intercropping of maize and pea in strips under various N managements was used as a means to alleviate the inhibitory effect of mineral N on pea nodulation and N2 fixation and to improve system performance.Methods
N natural abundance (δ 15N) analysis was employed to quantify N2 fixation in the 3 years (2012 to 2014) of field experiment in Hexi Corridor of Northwestern China. Four N management systems with N rate of 0 kg N ha?1 (the control), 90?+?45 kg N ha?1 (base N plus topdressing N), 90?+?90 kg N ha?1, and 90?+?135 kg N ha?1 were implemented in the maize/pea strip intercropping to form different ratios of base N to topdressing N.Results
Intercropped pea improved nodule biomass per plant by 99 %, increased nitrogen derived from the atmosphere (Ndfa) by 35 %, and promoted aboveground plant tissue N accumulation by 35 % as compared with sole pea, averaged across the four N treatments. Compared to the highest N fertilizer treatment, a reduction of topdressing to 45 kg N ha?1 increased the nodule biomass of intercropped pea by 116 %, Ndfa by 35 %, and grain yield by 6 %.Conclusions
Adaptation of suitable N management in cereal/legume intercropping systems will allow an effective conversion of atmospheric N2 into crop available N and thus maximizing the system productivity.13.
Paulin N. Wahjudi Qing-Yi Lu Mary E. Patterson Xuemei Zhang Vay Liang Go Jian Chen Wei-Lin Li W. N. Paul Lee 《Metabolomics : Official journal of the Metabolomic Society》2017,13(8):91
Introduction
Loquat leaf extract (LLE) is commonly used in China for a variety of ailments including diabetes. Several recent reports implicate LLE and a sesquiterpene glycoside, one of its components, as being an anti-hyperglycemic agent. However, the underlying mechanism of action of this anti-hyperglycemic agent has not been reported.Objective
We have conducted a tracer-based metabolomics study to investigate the effects of sesquiterpene and loquat extract on the balance of flux of central glucose metabolism in HepG2 cells and to compare with those of “insulin sensitizers”, metformin and rosiglitazone.Methods
Human hepatoma HepG2 cells in confluence culture were incubated in Dulbecco’s modified Eagle’s medium containing 50% [1, 2 13C2]-glucose in the presence of rosiglitazone, metformin, LLE or pure sesquiterpene. Cells were harvested in 48 h. Mass isotopomers of metabolites (glycogen, ribose, deoxyribose, glutamate and palmitate) were determined.Results
13C labeling in metabolic intermediates were summarized in a mass isotopomer matrix. Treatment with loquat extract/sesquiterpene, metformin and rosiglitazone each produced distinctive mass isotopomer patterns reflecting disparate effects on the contribution of glucose to various metabolites production, and on several metabolic flux ratios. The overall effect of LLE and sesquiterpene on glucose metabolism is clearly different from those of the known “insulin sensitizers”.Conclusion
Our study demonstrates the utility of isotopomer matrix in summarizing metabolic actions of LLE on the balance of fluxes occurring within the central glucose metabolism in HepG2 cells. 13C carbon tracing (tracer-based metabolomics) is a useful systems biology tool to elucidate glucose metabolic pathways affected by diabetes and its treatment.14.
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.15.
D. Jacob C. Deborde M. Lefebvre M. Maucourt A. Moing 《Metabolomics : Official journal of the Metabolomic Society》2017,13(4):36
Introduction
Concerning NMR-based metabolomics, 1D spectra processing often requires an expert eye for disentangling the intertwined peaks.Objectives
The objective of NMRProcFlow is to assist the expert in this task in the best way without requirement of programming skills.Methods
NMRProcFlow was developed to be a graphical and interactive 1D NMR (1H & 13C) spectra processing tool.Results
NMRProcFlow (http://nmrprocflow.org), dedicated to metabolic fingerprinting and targeted metabolomics, covers all spectra processing steps including baseline correction, chemical shift calibration and alignment.Conclusion
Biologists and NMR spectroscopists can easily interact and develop synergies by visualizing the NMR spectra along with their corresponding experimental-factor levels, thus setting a bridge between experimental design and subsequent statistical analyses.16.
Objective
To protect the enzymes during fed-batch cellulase production by means of partial enzyme recovery at regular intervals.Results
Extracellular enzymes were partially recovered at the intervals of 1, 2, or 3 days. Mycelia were also removed to avoid contamination. Increases in the total harvested cellulase (24–62%) and β-glucosidase (22–76%) were achieved. In fermentor cultivation when the enzymes were recovered every day with 15% culture broth. The total harvested cellulase and β-glucosidase activity increased by 43 and 58%, respectively, with fungal cell concentration maintained at 3.5–4.5 g l?1.Conclusion
Enzyme recovery at regular intervals during fed-batch cellulase cultivation could protect the enzyme in the culture broth and enhance the enzyme production when the fungal cell concentration is maintained in a reasonable range.17.
pH as a proxy for estimating plant-available Si? A case study in rice fields in Karnataka (South India) 总被引:1,自引:0,他引:1
Jean-Dominique Meunier Kollalu Sandhya Nagabovanalli B. Prakash Daniel Borschneck Philippe Dussouillez 《Plant and Soil》2018,431(1-2):143-157
Background and aims
Soil nutrient dynamics are affected by root-microbe interactions and plant development. We investigated the influence of plant growth stage and arbuscular mycorrhiza fungi (AMF) on carbon (C) and nitrogen (N) rhizodeposition and the transfer into the microbial biomass (MB).Methods
Pea varieties (Pisum sativum L.) with (Frisson) and without mycorrhiza (P2) were 13C-15N-labelled and harvested at 45, 63, 71, and 95 days after sowing. Mycorrhization, MB, total C, N, 13C, 15N were determined in plant and soil compartments to calculate C and N derived from rhizodeposition (CdfR, NdfR).Results
Total CdfR increased until pea maturity, NdfR until end of flowering. Their relative contribution steadily decreased over time, accounting for 4–10% of total plant C and N at harvest. Rhizodeposition contributed between 1 and 6% to MB C and N, although 20% of the rhizodeposits were discovered in the MB. Frisson released more NdfR than P2 but it was not possible to accurately estimate AMF effects on C and N due to differences in biomass partitioning.Conclusions
CdfR followed an even flow from early growth until senescence. NdfR flow ceased after flowering possibly due to N relocation within the plant. Rhizodeposits contribute very little to MB in our study.18.
Teklab Gebregiworgis Fatema Bhinderwala Vinee Purohit Nina V. Chaika Pankaj K. Singh 《Metabolomics : Official journal of the Metabolomic Society》2018,14(12):156
Introduction
Gemcitabine is an important component of pancreatic cancer clinical management. Unfortunately, acquired gemcitabine resistance is widespread and there are limitations to predicting and monitoring therapeutic outcomes.Objective
To investigate the potential of metabolomics to differentiate pancreatic cancer cells that develops resistance or respond to gemcitabine treatment.Results
We applied 1D 1H and 2D 1H–13C HSQC NMR methods to profile the metabolic signature of pancreatic cancer cells. 13C6-glucose labeling identified 30 key metabolites uniquely altered between wild-type and gemcitabine-resistant cells upon gemcitabine treatment. Gemcitabine resistance was observed to reprogram glucose metabolism and to enhance the pyrimidine synthesis pathway. Myo-inositol, taurine, glycerophosphocholine and creatinine phosphate exhibited a “binary switch” in response to gemcitabine treatment and acquired resistance.Conclusion
Metabolic differences between naïve and resistant pancreatic cancer cells and, accordingly, their unique responses to gemcitabine treatment were revealed, which may be useful in the clinical setting for monitoring a patient’s therapeutic response.19.
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.20.
Caroline Ivanne Le Roy Luke John Mappley Roberto Marcello La Ragione Martin John Woodward Sandrine Paule Claus 《Metabolomics : Official journal of the Metabolomic Society》2016,12(10):157