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Sheng Qin Wei-Wei Feng Tian-Tian Wang Peng Ding Ke Xing Ji-Hong Jiang 《Plant and Soil》2017,415(1-2):117-130
Background and aims
Xylem-tapping mistletoes may experience relaxed selective pressure to use water efficiently during photosynthesis because of lower per-unit costs for water acquisition than experienced by host plants. As a result, we hypothesised that mistletoes would exhibit parallel but dampened leaf-level adaptations and responses to aridity, compared to those seen in hosts.Methods
Photosynthetic traits, leaf dark respiration, nutrient concentrations and specific leaf area (SLA) were measured on 42 mistletoe-host species-pairs sampled from five sites in Australia and Brazil that vary widely in aridity.Results
Mistletoes exhibited similar trait-shifts to hosts in relation to site aridity. In both groups, arid-site species showed stronger control over stomatal water loss, larger drawdown of CO2 during photosynthesis (lower ci: ca), higher leaf N and P concentrations per unit leaf area, and lower SLA. Nevertheless, mistletoes were profligate water users compared to their hosts and showed substantially less efficient use of water during photosynthesis. On average, mistletoes showed twice higher leaf dark respiration rates at a given photosynthetic capacity, suggesting relatively higher leaf maintenance costs for these parasitic plants.Conclusions
Despite fundamental differences in lifestyle and in photosynthetic traits, mistletoes exhibit trait responses and adaptations to site aridity in parallel and to approximately the same extent as their hosts.3.
Wentao Luo Jordi Sardans Feike A. Dijkstra Josep Peñuelas Xiao-Tao Lü Honghui Wu Mai-He Li Edith Bai Zhengwen Wang Xingguo Han Yong Jiang 《Plant and Soil》2016,399(1-2):159-178
Background and aims
Aridity has increased in the past decades and will probably continue to increase in arid and semiarid regions. Here we decipher the plant and soil capacity to retain metal cations when climate evolves to more arid conditions.Methods
We analyzed K, Na, Ca, Mg, Fe, Mn, Zn and Cu concentrations in 580 soil samples and 666 plant (shoot and root) samples along a 3600 km aridity gradient in northern China.Results
The concentrations of soil exchangeable K, Mg, Mn, Fe and Cu clearly decreased with increasing aridity due to the relationships of aridity with soil clay content and soil pH. Increases in exchangeable Na and Ca concentrations at mid- and high-aridity levels are probably due to the soil salinization, whereas increased exchangeable Fe concentrations at extreme levels of aridity may be more related to a reduced pH. Element concentrations in both plant shoots and roots were unrelated to soil exchangeable element concentrations; instead they increased monotonously with increasing aridity, corresponding with decreases in plant size and shoot/root ratios. The shoot/root mineralomass ratios in general increased with increasing aridity. The proportional higher element contents in shoots than in roots with increasing aridity are related to increased water uptake and/or use efficiency.Conclusions
The extractability of soil elements in response to changing climate varied with the nature of specific elements that are controlled by biological and geochemical processes, i.e., some decreased linearly with increasing aridity, whereas others first decreased and then increased with different thresholds. These contrasting effects of aridity on nutrient availability could further constrain plant growth and should be incorporated into biogeochemical models. The prevailing paradigm of a positive relationship between concentrations of plant and soil elements needs to be reconsidered under changing climatic conditions.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.
Background
Cerebral infarction caused by different reasons seems differ in fibrinogen levels, so the current work intends to explore the relationship between the fibrinogen level and subtypes of the TOAST criteria in the acute stage of ischemic stroke.Methods
A total of 577 case research objects were treated acute ischemic stroke patients in our hospital from December 2008 to December 2010, and blood samples within 72 hours of the onset were processed with the fibrinogen (PT-der) measurement. Classification of selected patients according to the TOAST Criteria was conducted to study the distribution of fibrinogen levels in the stroke subtypes.Results
The distribution of fibrinogen levels in the subtypes was observed to be statistically insignificant.Conclusions
In the acute stage of ischemic stroke, fibrinogen level was not related to the subtypes of the TOAST criteria.6.
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.7.
Maria L. F. Ternes Leopoldo C. Gerhardinger Alexandre Schiavetti 《Journal of ethnobiology and ethnomedicine》2016,12(1):52
Background
Seahorses are endangered teleost fishes under increasing human pressures worldwide. In Brazil, marine conservationists and policy-makers are thus often skeptical about the viability of sustainable human-seahorse interactions. This study focuses on local ecological knowledge on seahorses and the implications of their non-lethal touristic use by a coastal community in northeastern Brazil. Community-based seahorse-watching activities have been carried out in Maracaípe village since 1999, but remained uninvestigated until the present study. Our goal is to provide ethnoecological understanding on this non-extractive use to support seahorse conservation and management.Methods
We interviewed 32 informants through semi-structured questionnaires to assess their socioeconomic profile, their knowledge on seahorse natural history traits, human uses, threats and abundance trends.Results
Seahorse-watching has high socioeconomic relevance, being the primary income source for all respondents. Interviewees elicited a body of knowledge on seahorse biology largely consistent with up-to-date research literature. Most informants (65.5 %) perceived no change in seahorse abundance. Their empirical knowledge often surpassed scientific reports, i.e. through remarks on trophic ecology; reproductive aspects, such as, behavior and breeding season; spatial and temporal distribution, suggesting seahorse migration related to environmental parameters.Conclusions
Seahorse-watching operators were aware of seahorse biological and ecological aspects. Despite the gaps remaining on biological data about certain seahorse traits, the respondents provided reliable information on all questions, adding ethnoecological remarks not yet assessed by conventional scientific surveys. We provide novel ethnobiological insight on non-extractive modes of human-seahorse interaction, eliciting environmental policies to integrate seahorse conservation with local ecological knowledge and innovative ideas for seahorse sustainable use. Our study resonates with calls for more active engagement with communities and their local ecologies if marine conservation and development are to be reconciled.8.
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.9.
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.10.
Background
Data integration is a crucial task in the biomedical domain and integrating data sources is one approach to integrating data. Data elements (DEs) in particular play an important role in data integration. We combine schema- and instance-based approaches to mapping DEs to terminological resources in order to facilitate data sources integration.Methods
We extracted DEs from eleven disparate biomedical sources. We compared these DEs to concepts and/or terms in biomedical controlled vocabularies and to reference DEs. We also exploited DE values to disambiguate underspecified DEs and to identify additional mappings.Results
82.5% of the 474 DEs studied are mapped to entries of a terminological resource and 74.7% of the whole set can be associated with reference DEs. Only 6.6% of the DEs had values that could be semantically typed.Conclusion
Our study suggests that the integration of biomedical sources can be achieved automatically with limited precision and largely facilitated by mapping DEs to terminological resources.11.
Background
The DNase I hypersensitive sites (DHSs) are associated with the cis-regulatory DNA elements. An efficient method of identifying DHSs can enhance the understanding on the accessibility of chromatin. Despite a multitude of resources available on line including experimental datasets and computational tools, the complex language of DHSs remains incompletely understood.Methods
Here, we address this challenge using an approach based on a state-of-the-art machine learning method. We present a novel convolutional neural network (CNN) which combined Inception like networks with a gating mechanism for the response of multiple patterns and longterm association in DNA sequences to predict multi-scale DHSs in Arabidopsis, rice and Homo sapiens.Results
Our method obtains 0.961 area under curve (AUC) on Arabidopsis, 0.969 AUC on rice and 0.918 AUC on Homo sapiens.Conclusions
Our method provides an efficient and accurate way to identify multi-scale DHSs sequences by deep learning.12.
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.13.
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.14.
Sonia Liggi Christine Hinz Zoe Hall Maria Laura Santoru Simone Poddighe John Fjeldsted Luigi Atzori Julian L. Griffin 《Metabolomics : Official journal of the Metabolomic Society》2018,14(4):52
Introduction
Data processing is one of the biggest problems in metabolomics, given the high number of samples analyzed and the need of multiple software packages for each step of the processing workflow.Objectives
Merge in the same platform the steps required for metabolomics data processing.Methods
KniMet is a workflow for the processing of mass spectrometry-metabolomics data based on the KNIME Analytics platform.Results
The approach includes key steps to follow in metabolomics data processing: feature filtering, missing value imputation, normalization, batch correction and annotation.Conclusion
KniMet provides the user with a local, modular and customizable workflow for the processing of both GC–MS and LC–MS open profiling data.15.
Ferran Casbas Pinto Srinivarao Ravipati David A. Barrett T. Charles Hodgman 《Metabolomics : Official journal of the Metabolomic Society》2017,13(7):81
Introduction
It is difficult to elucidate the metabolic and regulatory factors causing lipidome perturbations.Objectives
This work simplifies this process.Methods
A method has been developed to query an online holistic lipid metabolic network (of 7923 metabolites) to extract the pathways that connect the input list of lipids.Results
The output enables pathway visualisation and the querying of other databases to identify potential regulators. When used to a study a plasma lipidome dataset of polycystic ovary syndrome, 14 enzymes were identified, of which 3 are linked to ELAVL1—an mRNA stabiliser.Conclusion
This method provides a simplified approach to identifying potential regulators causing lipid-profile perturbations.16.
Nadine Strehmel David Strunk Veronika Strehmel 《Metabolomics : Official journal of the Metabolomic Society》2017,13(11):135
Introduction
Aqueous–methanol mixtures have successfully been applied to extract a broad range of metabolites from plant tissue. However, a certain amount of material remains insoluble.Objectives
To enlarge the metabolic compendium, two ionic liquids were selected to extract the methanol insoluble part of trunk from Betula pendula.Methods
The extracted compounds were analyzed by LC/MS and GC/MS.Results
The results show that 1-butyl-3-methylimidazolium acetate (IL-Ac) predominantly resulted in fatty acids, whereas 1-ethyl-3-methylimidazolium tosylate (IL-Tos) mostly yielded phenolic structures. Interestingly, bark yielded more ionic liquid soluble metabolites compared to interior wood.Conclusion
From this one can conclude that the application of ionic liquids may expand the metabolic snapshot.17.
Thijs Welle Anna T. Hoekstra Ineke A. J. J. M. Daemen Celia R. Berkers Matheus O. Costa 《Metabolomics : Official journal of the Metabolomic Society》2017,13(7):83
Introduction
Swine dysentery caused by Brachyspira hyodysenteriae is a production limiting disease in pig farming. Currently antimicrobial therapy is the only treatment and control method available.Objective
The aim of this study was to characterize the metabolic response of porcine colon explants to infection by B. hyodysenteriae.Methods
Porcine colon explants exposed to B. hyodysenteriae were analyzed for histopathological, metabolic and pro-inflammatory gene expression changes.Results
Significant epithelial necrosis, increased levels of l-citrulline and IL-1α were observed on explants infected with B. hyodysenteriae.Conclusions
The spirochete induces necrosis in vitro likely through an inflammatory process mediated by IL-1α and NO.18.
19.
Roberto Stella Gaud Dervilly-Pinel Davide Bovo Eleonora Mastrorilli Anne-Lise Royer Roberto Angeletti Bruno Le Bizec Giancarlo Biancotto 《Metabolomics : Official journal of the Metabolomic Society》2017,13(7):80
Introduction
The surveillance of illegal anabolic practices in bovine meat production is necessary to guarantee consumers’ health. Screening strategies based on the recognition of indirect biological effects are considered by the community as promising tools to overcome some limitations of classical analytical methods and might therefore concur to ensure safer food for the consumer.Objectives
The present work aims at characterizing the metabolic profile induced in liver by administration of anabolic steroids, and at identifying potential disturbances in the hepatic metabolism.Methods
A total of 32 liver samples, 16 from untreated bulls and 16 from bulls treated with an ear implant (Revalor-XS®) containing trenbolone acetate (200 mg) and β-estradiol (40 mg), were analyzed following a LC–MS-based metabolomic analysis combining RP and HILIC chromatographic separations. Different multivariate statistical tools were applied to the datasets to select common metabolites that may be considered as potential markers based on their significant changes in concentrations after administration of sexual steroids.Results
Eight candidate markers were identified. Moreover, a subset of four markers was also validated by a different laboratory that performed the same analysis using an independent instrumental and elaboration platform, confirming the robustness of the results achieved.Conclusion
This study was performed mimicking experimental conditions that may be used during a potential misuse practice. It is promising in the objective of setting up an analytical strategy to highlight sexual steroids abuse in livestock animals.20.
Rob van Treuren Henriette D. L. M. van Eekelen Ron Wehrens Ric C. H. de Vos 《Metabolomics : Official journal of the Metabolomic Society》2018,14(11):146