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1.
Background and aims
In Malawi, strategies are being sought to boost maize production through improvements in soil fertility. This study assessed the impact of intercropping maize (Zea mays) with pigeon pea (Cajanus cajan) in Lixisols of Malawi on yield, biological N fixation, soil aggregation, and P forms within soil aggregates.Methods
Maize and pigeon pea were grown intercropped in pots, with varying degrees of root interaction in order to understand the relative importance of biochemical versus physical rhizospheric interactions. Following harvest, soils were separated into aggregate fractions using wet-sieving, and the nutrient content of all fractions was assessed.Results
The proportion of macroaggregates and microaggregates increased by 52 and 111%, respectively, in the intercropping treatment compared to sole maize, which significantly increased organic P storage in the microaggregates of intercropped compared to sole maize (84 versus 29 mg P kg?1, respectively). Biologically fixed N increased from 89% in the sole pigeon pea to 96% in the intercropped system.Conclusions
Intercropping maize with pigeon pea can have a significant and positive impact on soil structure as well as nutrient storage in these high P-sorbing soils. This is caused primarily by physical root contact and to a lesser degree by biochemical activities.2.
Korey J. Brownstein Mahmoud Gargouri William R. Folk David R. Gang 《Metabolomics : Official journal of the Metabolomic Society》2017,13(11):133
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.3.
Marie J. Zwetsloot Johannes Lehmann Taryn Bauerle Steven Vanek Rachel Hestrin Abebe Nigussie 《Plant and Soil》2016,408(1-2):95-105
Aims
The objectives of this study were to evaluate (1) the fertilizer potential of bone char, (2) the effects of wood biochar on plant-available phosphorus (P), and (3) the role of root-mycorrhizae-biochar interactions in plant P acquisition from a P-fixing soil.Methods
Incubation and pot experiments were conducted with a P-fixing soil and maize with or without root hairs and arbuscular mycorrhizae (AM) inoculation. Olsen-, resin-P and plant P accumulation were used to estimate P availability from bone char, co-pyrolyzed bone char-wood biochar, and separate bone char and wood biochar additions produced at 60, 350 and 750 °C, and Triple Superphosphate (TSP).Results
Maize inoculated with AM showed similar P accumulation when fertilized with either 750 °C bone char or TSP. Pyrolyzing bone did not increase extractable P in soil in comparison to unpyrolyzed bone, apart from a 67 % increase in resin-extractable P after additions of bone char pyrolyzed at 350 °C. Despite greater Olsen-P extractability, co-pyrolysis of bone with wood reduced maize P uptake. Wood biochars reduced resin-P from bone char by 14–26 %, whereas oven-dried wood increased resin-P by 23 %.Conclusions
Bone char is an effective P fertilizer, especially if root-AM interactions are simultaneously considered. Biochar influences plant access to soil P and requires careful management to improve P availability.4.
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.5.
Yuan Wang Xue-Yin Zhang Yan-Ling Luo Feng Xu Ya-Shao Chen Yu-Yu Su 《Journal of nanobiotechnology》2017,15(1):76
Background
Stimuli-responsive polymer materials are a new kind of intelligent materials based on the concept of bionics, which exhibits more significant changes in physicochemical properties upon triggered by tiny environment stimuli, hence providing a good carrier platform for antitumor drug delivery.Results
Dual stimuli-responsive Fe3O4 graft poly(acrylic acid)-block-poly(2-methacryloyloxyethyl ferrocenecarboxylate) block copolymers (Fe3O4-g-PAA-b-PMAEFC) were engineered and synthesized through a two-step sequential reversible addition-fragmentation chain transfer polymerization route. The characterization was performed by FTIR, 1H NMR, SEC, XRD and TGA techniques. The self-assembly behavior in aqueous solution upon triggered by pH, magnetic and redox stimuli was investigated via zeta potentials, vibration sample magnetometer, cyclic voltammetry, fluorescent spectrometry, dynamic light scattering, XPS, TEM and SEM measurements. The experimental results indicated that the Fe3O4-g-PAA-b-PMAEFC copolymer materials could spontaneously assemble into hybrid magnetic copolymer micromicelles with core–shell structure, and exhibited superparamagnetism, redox and pH stimuli-responsive features. The hybrid copolymer micromicelles were stable and nontoxic, and could entrap hydrophobic anticancer drug, which was in turn swiftly and effectively delivered from the drug-loaded micromicelles at special microenvironments such as acidic pH and high reactive oxygen species.Conclusion
This class of stimuli-responsive copolymer materials is expected to find wide applications in medical science and biology, etc., especially in drug delivery system.6.
Leonie Venter Du Toit Loots Lodewyk Japie Mienie Peet J. Jansen van Rensburg Shayne Mason Andre Vosloo Jeremie Zander Lindeque 《Metabolomics : Official journal of the Metabolomic Society》2018,14(4):49
Introduction
Oxygen is essential for metabolic processes and in the absence thereof alternative metabolic pathways are required for energy production, as seen in marine invertebrates like abalone. Even though hypoxia has been responsible for significant losses to the aquaculture industry, the overall metabolic adaptations of abalone in response to environmental hypoxia are as yet, not fully elucidated.Objective
To use a multiplatform metabolomics approach to characterize the metabolic changes associated with energy production in abalone (Haliotis midae) when exposed to environmental hypoxia.Methods
Metabolomics analysis of abalone adductor and foot muscle, left and right gill, hemolymph, and epipodial tissue samples were conducted using a multiplatform approach, which included untargeted NMR spectroscopy, untargeted and targeted LC–MS spectrometry, and untargeted and semi-targeted GC-MS spectrometric analyses.Results
Increased levels of anaerobic end-products specific to marine animals were found which include alanopine, strombine, tauropine and octopine. These were accompanied by elevated lactate, succinate and arginine, of which the latter is a product of phosphoarginine breakdown in abalone. Primarily amino acid metabolism was affected, with carbohydrate and lipid metabolism assisting with anaerobic energy production to a lesser extent. Different tissues showed varied metabolic responses to hypoxia, with the largest metabolic changes in the adductor muscle.Conclusions
From this investigation, it becomes evident that abalone have well-developed (yet understudied) metabolic mechanisms for surviving hypoxic periods. Furthermore, metabolomics serves as a powerful tool for investigating the altered metabolic processes in abalone.7.
Nikolaos Thomakos Khandra Galaal Georgios Georgopoulos Lakshmi Nagaraju Dianne Hemming Raj Naik 《International Seminars in Surgical Oncology : ISSO》2009,6(1):3
Background
Choroidal metastases from gynaecological primary are extremely rare. There is no documented case in the literature of choroid metastasis in a patient with primary peritoneal carcinoma (PPC).Methods & Results
We describe the first case of a 54-year-old woman with a history of borderline mucinous tumour who presented 17 months later with PPC and 21 months after with recurrent disease metastatic to the eye, and review pertinent literature.Conclusion
High index of suspicion is warranted when patients with history of primary peritoneal carcinoma present with visual complaints in order to treat and/or relieve symptomatology from metastatic eye disease.8.
9.
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.10.
11.
Edoardo Saccenti Age K. Smilde José Camacho 《Metabolomics : Official journal of the Metabolomic Society》2018,14(6):73
Introduction
Modern omics experiments pertain not only to the measurement of many variables but also follow complex experimental designs where many factors are manipulated at the same time. This data can be conveniently analyzed using multivariate tools like ANOVA-simultaneous component analysis (ASCA) which allows interpretation of the variation induced by the different factors in a principal component analysis fashion. However, while in general only a subset of the measured variables may be related to the problem studied, all variables contribute to the final model and this may hamper interpretation.Objectives
We introduce here a sparse implementation of ASCA termed group-wise ANOVA-simultaneous component analysis (GASCA) with the aim of obtaining models that are easier to interpret.Methods
GASCA is based on the concept of group-wise sparsity introduced in group-wise principal components analysis where structure to impose sparsity is defined in terms of groups of correlated variables found in the correlation matrices calculated from the effect matrices.Results
The GASCA model, containing only selected subsets of the original variables, is easier to interpret and describes relevant biological processes.Conclusions
GASCA is applicable to any kind of omics data obtained through designed experiments such as, but not limited to, metabolomic, proteomic and gene expression data.12.
Gustavo Boitt Amanda Black Steve A. Wakelin Richard W. McDowell Leo M. Condron 《Plant and Soil》2018,427(1-2):163-174
Aims
We assessed and quantified the cumulative impact of 20 years of biomass management on the nature and bioavailability of soil phosphorus (P) accumulated from antecedent fertiliser inputs.Methods
Soil (0–2.5, 2.5–5, 5–10 cm) and plant samples were taken from replicate plots in a grassland field experiment maintained for 20 years under contrasting plant biomass regimen- biomass retained or removed after mowing. Analyses included dry matter production and P uptake, root biomass, total soil carbon (C), total nitrogen (N), total P, soil P fractionation, and 31P NMR spectroscopy.Results
Contemporary plant production and P uptake were over 2-fold higher for the biomass retained compared with the biomass removed regimes. Soil C, total P, soluble and labile forms of inorganic and organic soil P were significantly higher under biomass retention than removal.Conclusions
Reserves of soluble and labile inorganic P in soil were significantly depleted in response to continued long-term removal of P in plant biomass compared to retention. However, this was only sufficient to sustain plant production at half the level observed for the biomass retention after 20 years, which was partly attributed to limited mobilisation of organic P in response to P removal.13.
Margarita Stritzler Ana Diez Tissera Gabriela Soto Nicolás Ayub 《Biotechnology letters》2018,40(9-10):1419-1423
Objectives
Identification of novel microbial factors contributing to plant protection against abiotic stress.Results
The genome of plant growth-promoting bacterium Pseudomonas fluorescens FR1 contains a short mobile element encoding a novel type of extracellular polyhydroxybutyrate (PHB) polymerase (PhbC) associated with a type I secretion system. Genetic analysis using a phbC mutant strain and plants showed that this novel extracellular enzyme is related to the PHB production in planta and suggests that PHB could be a beneficial microbial compound synthesized during plant adaptation to cold stress.Conclusion
Extracellular PhbC can be used as a new tool for improve crop production under abiotic stress.14.
Objective
To examine the activities of residual enzymes in dried shiitake mushrooms, which are a traditional foodstuff in Japanese cuisine, for possible applications in food processing.Results
Polysaccharide-degrading enzymes remained intact in dried shiitake mushrooms and the activities of amylase, β-glucosidase and pectinase were high. A potato digestion was tested using dried shiitake powder. The enzymes reacted with potato tuber specimens to solubilize sugars even under a heterogeneous solid-state condition and that their reaction modes were different at 38 and 50 °C.Conclusion
Dried shiitake mushrooms have a potential use in food processing as an enzyme preparation.15.
Strategies to assess and optimize stability of endogenous amines during cerebrospinal fluid sampling
Marek J. Noga Ronald Zielman Robin M. van Dongen Sabine Bos Amy Harms Gisela M. Terwindt Arn M. J. M. van den Maagdenberg Thomas Hankemeier Michel D. Ferrari 《Metabolomics : Official journal of the Metabolomic Society》2018,14(4):44
Introduction
Metabolic profiling of cerebrospinal fluid (CSF) is a promising technique for studying brain diseases. Measurements should reflect the in vivo situation, so ex vivo metabolism should be avoided.Objective
To investigate the effects of temperature (room temperature vs. 4 °C), centrifugation and ethanol, as anti-enzymatic additive during CSF sampling on concentrations of glutamic acid, glutamine and other endogenous amines.Methods
CSF samples from 21 individuals were processed using five different protocols. Isotopically-labeled alanine, isoleucine, glutamine, glutamic acid and dopamine were added prior to sampling to trace any degradation. Metabolomics analysis of endogenous amines, isotopically-labeled compounds and degradation products was performed with a validated LC–MS method.Results
Thirty-six endogenous amines were quantified. There were no statistically significant differences between sampling protocols for 31 out of 36 amines. For GABA there was primarily an effect of temperature (higher concentrations at room temperature than at 4 °C) and a small effect of ethanol (lower concentrations if added) due to possible degradation. O-phosphoethanolamine concentrations were also lower when ethanol was added. Degradation of isotopically-labeled compounds (e.g. glutamine to glutamic acid) was minor with no differences between protocols.Conclusion
Most amines can be considered stable during sampling, provided that samples are cooled immediately to 4 °C, centrifuged, and stored at ??80 °C within 2 h. The effect of ethanol addition for more unstable metabolites needs further investigation. This was the first time that labeled compounds were used to monitor ex vivo metabolism during sampling. This is a useful strategy to study the stability of other metabolites of interest.16.
Objective
To investigate the effects of heat-killed Enterococcus faecalis ATCC 29212 and P25RC clinical strain (derived from an obturated root canal with apical periodontitis) on osteoclast differentiation within an osteoblast/osteoclast co-culture system.Results
Heat-killed E. faecalis significantly increased the proportion of multinucleated osteoclastic cells (MNCs) within the co-culture system. The IL-6 level was significantly increased upon exposure to heat-killed E. faecalis. Gene expression levels of NFATc1 and cathepsin K were significantly up-regulated compared to the untreated control. EphrinB2 and EphB4 expressions at both the mRNA and protein levels were also significantly upregulated compared to the untreated control.Conclusions
Heat-killed E. faecalis can induce osteoclast differentiation within the osteoblast/osteoclast co-culture system in vitro, possibly through ephrinB2-EphB4 bidirectional signaling.17.
Hailong Zhang Longzhen Cui Wen Liu Zhenfeng Wang Yang Ye Xue Li Huijuan Wang 《Metabolomics : Official journal of the Metabolomic Society》2018,14(4):47
Introduction
Gastric cancer (GC) is a malignant tumor worldwide. As primary pathway for metastasis, the lymphatic system is an important prognostic factor for GC patients. Although the metabolic changes of gastric cancer have been investigated in extensive studies, little effort focused on the metabolic profiling of lymph node metastasis (LNM)-positive or negative GC patients.Objectives
We performed 1H NMR spectrum of GC tissue samples with and without LNM to identify novel potential metabolic biomarkers in the process of LNM of GC.Methods
1H NMR-based untargeted metabolomics approach combined with multivariate statistical analyses were used to study the metabolic profiling of tissue samples from LNM-positive GC patients (n?=?40), LNM-negative GC patients (n?=?40) and normal controls (n?=?40).Results
There was a clear separation between GC patients and normal controls, and 33 differential metabolites were identified in the study. Moreover, GC patients were also well-classified according to LNM-positive or negative. Totally eight distinguishing metabolites were selected in the metabolic profiling of GC patients with LNM-positive or negative, suggesting the metabolic dysfunction in the process of LNM. According to further validation and analysis, especially BCAAs metabolism (leucine, isoleucine, valine), GSH and betaine may be as potential factors of diagnose and prognosis of GC patients with or without LNM.Conclusion
To our knowledge, this is the first metabolomics study focusing on LNM of GC. The identified distinguishing metabolites showed a promising application on clinical diagnose and therapy prediction, and understanding the mechanism underlying the carcinogenesis, invasion and metastasis of GC.18.
Background
Intermittent preventive treatment (IPT) has recently been accepted as an important component of the malaria control strategy. Intermittent preventive treatment for children (IPTc) combined with timely treatment of malaria related febrile illness at home to reduce parasite prevalence and malaria morbidity in children aged between six and 60 months in a coastal community in Ghana. This paper reports persistence of reduced parasitaemia two years into the intervention. The baseline and year-one-evaluation findings were published earlier.Objective
The main objective in the second year was to demonstrate whether the two interventions would further reduce parasite prevalence and malaria-related febrile illness in the study population.Methods
This was an intervention study designed to compare baseline and evaluation findings without a control group. The study combined home-based delivery of intermittent preventive treatment for children (IPTc) aged 6 - 60 months and home treatment of suspected febrile malaria-related illness within 24 hours. All children aged 6 - 60 months received home-based delivery of intermittent preventive treatment using amodiaquine + artesunate, delivered at home by community assistants every four months (6 times in 24 months). Malaria parasite prevalence surveys were conducted before the first and after the third and sixth IPTc to the children. The evaluation surveys were done four months after the third and sixth IPTc was given.Results
Parasite prevalence which reduced from 25% to 3.0% at year-one evaluation had reduced further from 3% to 1% at year-two-evaluation. At baseline, 13.8% of the children were febrile (axilary temperature of ≥37.5°C) compared to 2.2% at year-one-evaluation while 2.1% were febrile at year-two-evaluation.Conclusion
The year-two-evaluation result indicates that IPTc given three times in a year (every four months) combined with timely treatment of febrile malaria illness, is effective to reduce malaria parasite prevalence in children aged 6 to 60 months in the study community. This must give hope to malaria control programme managers in sub-Saharan Africa where the burden of the disease is most debilitating.19.
Background
Orthostatic intolerance is common in chronic fatigue syndrome (CFS), and several studies have documented an abnormal sympathetic predominance in the autonomic cardiovascular response to gravitational stimuli. The aim of this study was to explore whether the expectancies towards standing are contributors to autonomic responses in addition to the gravitational stimulus itself.Methods
A total of 30 CFS patients (12–18 years of age) and 39 healthy controls underwent 20° head-up tilt test and a motor imagery protocol of standing upright. Beat-to-beat cardiovascular variables were recorded.Results
At supine rest, CFS patients had significantly higher heart rate, diastolic blood pressure, and mean arterial blood pressure, and lower stroke index and heart rate variability (HRV) indices. The response to 20° head-up tilt was identical in the two groups. The response to imaginary upright position was characterized by a stronger increase of HRV indices of sympathetic predominance (power in the low-frequency range as well as the ratio low-frequency: high-frequency power) among CFS patients.Conclusions
These results suggest that in CFS patients expectancies towards orthostatic challenge might be additional determinants of autonomic cardiovascular modulation along with the gravitational stimulus per se.20.
Bowen Li Meng Gou Jianmei Han Xiaofei Yuan Yingying Li Tiesong Li Qi Jiang Rong Xiao Qingwei Li 《Proteome science》2018,16(1):9