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1.
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.2.
3.
Douglas B. Kell Stephen G. Oliver 《Metabolomics : Official journal of the Metabolomic Society》2016,12(9):148
Background
The term ‘metabolome’ was introduced to the scientific literature in September 1998.Aim and key scientific concepts of the review
To mark its 18-year-old ‘coming of age’, two of the co-authors of that paper review the genesis of metabolomics, whence it has come and where it may be going.4.
Background
Pseudomyxoma peritonei is a rare condition consisting of mucinous ascites, most commonly arising from mucinous tumors of the appendix and occasionally from the ovary. Very rarely mucinous implants arise in the retroperitoneum without any intra-peritoneal involvement. This has been termed as pseudomyxoma extraperitonei.Case presentation
We report a case of a 57 year old man who developed pseudomyxoma extraperitonei, 35 years after undergoing an appendicectomy for a perforated appendix.Conclusions
Pseudomyxoma extraperitonei has been previously reported, however we report the longest incubation period of 35 years for this condition.5.
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.6.
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.7.
Gunjal Garg Ali Yilmaz Praveen Kumar Onur Turkoglu David G. Mutch Matthew A. Powell Barry Rosen Ray O. Bahado-Singh Stewart F. Graham 《Metabolomics : Official journal of the Metabolomic Society》2018,14(12):154
Introduction
Epithelial ovarian cancer (EOC) remains the leading cause of death from gynecologic malignancies and has an alarming global fatality rate. Besides the differences in underlying pathogenesis, distinguishing between high grade (HG) and low grade (LG) EOC is imperative for the prediction of disease progression and responsiveness to chemotherapy.Objectives
The aim of this study was to investigate, the tissue metabolome associated with HG and LG serous epithelial ovarian cancer.Methods
A combination of one dimensional proton nuclear magnetic resonance (1D H NMR) spectroscopy and targeted mass spectrometry (MS) was employed to profile the tissue metabolome of HG, LG serous EOCs, and controls.Results
Using partial least squares-discriminant analysis, we observed significant separation between all groups (p?<?0.05) following cross validation. We identified which metabolites were significantly perturbed in each EOC grade as compared with controls and report the biochemical pathways which were perturbed due to the disease. Among these metabolic pathways, ascorbate and aldarate metabolism was identified, for the first time, as being significantly altered in both LG and HG serous cancers. Further, we have identified potential biomarkers of EOC and generated predictive algorithms with AUC (CI)?=?0.940 and 0.929 for HG and LG, respectively.Conclusion
These previously unreported biochemical changes provide a framework for future metabolomic studies for the development of EOC biomarkers. Finally, pharmacologic targeting of the key metabolic pathways identified herein could lead to novel and effective treatments of EOC.8.
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.9.
Background
We investigated local knowledge of plants in terms of plant use shifts and losses, in two coastal communities within a protected area in southern Brazil. Our hypothesis is that people’s livelihoods are associated with different ethnobotanical knowledge, and changes in these activities can reflect shifts in ethnobotanical knowledge such as stopping using some plants.Methods
We interviewed 125 inhabitants after prior informed consent, asking her/him about their socioeconomic profile and to free list the plants they know. The free lists were analyzed by frequency of cited plants. To compare averages of cited plants and age in both communities, we used the Wilcoxon test with a significance of 5%. Spearman correlation was tested with number of plants cited in the past and the interviewees’ age. Permanence and change in economic activities in each community were represented using a graph and compared through a chi-squared test with a significance of 5%. Qualitative analyses of the interviews and a field diary were used to analyze driving forces for the abandonment of used plants.Results
We identified 231 plant species that were currently used mainly for food and medicine. Despite being in a protected area, most of the cited plants were exotic and cultivated in home gardens. We do not confirm the hypothesis that changes in livelihoods are reflected in the plants used; however, qualitative analyses showed potential drivers for shifts and losses of plant use. “Environmental law” and “protected area” were the drivers most related to the abandonment of plant use.Conclusions
While recognizing the importance of the protected area to maintain local people and their traditions, we documented a shift in plant use that is mainly correlated to construction activities that disappeared from daily practices.10.
Background and aims
Plant-soil feedback may vary across host species and environmental gradients. The relative importance of these biotic versus abiotic drivers of feedback will determine the stability of plant and microbial communities across environments. If plant hosts are the main driver of soil microbial communities, plant-soil feedback may be stable across changing environments. However, if microbial communities vary with environmental gradients, feedback may also vary, limiting its capacity to predict plant distributions.Methods
We characterized arbuscular mycorrhizal (AM) fungi across tree plantations and a primary Neotropical rainforest. We then performed a plant-soil feedback pot experiment of AM fungi from these plantations on three plant species and related feedback and AM fungal communities in the field.Results
In the field, temporal and spatial variation in AM fungal composition was similar in magnitude to variation across plant host species. Composition of AM fungi in the pot experiment significantly differed from the field plots. Furthermore, differential feedback was explained by shifts in AM fungal composition only for one plant host species (Hyeronima alchorneoides) in the pot experiment.Conclusions
Natural AM fungal communities were temporally and spatially heterogeneous and AM fungal communities in the greenhouse did not reflect natural soils. These factors led to heterogeneous and unpredictable feedback responses, which suggests that applying greenhouse derived plant-soil feedback trends to predict plant coexistence in natural systems may be misleading.11.
Background
Highly successful strategies to make populations more resilient to infectious diseases, such as childhood vaccinations programs, may nonetheless lead to unpredictable outcomes due to the interplay between seasonal variations in transmission and a population’s immune status.Methods
Motivated by the study of diseases such as pertussis we introduce a seasonally-forced susceptible-infectious-recovered model of disease transmission with waning and boosting of immunity. We study the system’s dynamical properties using a combination of numerical simulations and bifurcation techniques, paying particular attention to the properties of the initial condition space.Results
We find that highly unpredictable behaviour can be triggered by changes in biologically relevant model parameters such as the duration of immunity. In the particular system we analyse — previously used in the literature to study pertussis dynamics — we identify the presence of an initial-condition landscape containing three coexisting attractors. The system’s response to interventions which perturb population immunity (e.g. vaccination "catch-up" campaigns) is therefore difficult to predict.Conclusion
Given the increasing use of models to inform policy decisions regarding vaccine introduction and scheduling and infectious diseases intervention policy more generally, our findings highlight the importance of thoroughly investigating the dynamical properties of those models to identify key areas of uncertainty. Our findings suggest that the often stated tension between capturing biological complexity and utilising mathematically simple models is perhaps more nuanced than generally suggested. Simple dynamical models, particularly those which include forcing terms, can give rise to incredibly complex behaviour.12.
Background
Identification of phosphorylation sites by computational methods is becoming increasingly important because it reduces labor-intensive and costly experiments and can improve our understanding of the common properties and underlying mechanisms of protein phosphorylation.Methods
A multitask learning framework for learning four kinase families simultaneously, instead of studying each kinase family of phosphorylation sites separately, is presented in the study. The framework includes two multitask classification methods: the Multi-Task Least Squares Support Vector Machines (MTLS-SVMs) and the Multi-Task Feature Selection (MT-Feat3).Results
Using the multitask learning framework, we successfully identify 18 common features shared by four kinase families of phosphorylation sites. The reliability of selected features is demonstrated by the consistent performance in two multi-task learning methods.Conclusions
The selected features can be used to build efficient multitask classifiers with good performance, suggesting they are important to protein phosphorylation across 4 kinase families.13.
Dan Li William Yang Carolyn Arthur Jun S. Liu Carolina Cruz-Niera Mary Qu Yang 《BMC systems biology》2018,12(7):117
Background
Adenocarcinoma in situ (AIS) is a pre-invasive lesion in the lung and a subtype of lung adenocarcinoma. The patients with AIS can be cured by resecting the lesion completely. In contrast, the patients with invasive lung adenocarcinoma have very poor 5-year survival rate. AIS can develop into invasive lung adenocarcinoma. The investigation and comparison of AIS and invasive lung adenocarcinoma at the genomic level can deepen our understanding of the mechanisms underlying lung cancer development.Results
In this study, we identified 61 lung adenocarcinoma (LUAD) invasive-specific differentially expressed genes, including nine long non-coding RNAs (lncRNAs) based on RNA sequencing techniques (RNA-seq) data from normal, AIS, and invasive tissue samples. These genes displayed concordant differential expression (DE) patterns in the independent stage III LUAD tissues obtained from The Cancer Genome Atlas (TCGA) RNA-seq dataset. For individual invasive-specific genes, we constructed subnetworks using the Genetic Algorithm (GA) based on protein-protein interactions, protein-DNA interactions and lncRNA regulations. A total of 19 core subnetworks that consisted of invasive-specific genes and at least one putative lung cancer driver gene were identified by our study. Functional analysis of the core subnetworks revealed their enrichment in known pathways and biological progresses responsible for tumor growth and invasion, including the VEGF signaling pathway and the negative regulation of cell growth.Conclusions
Our comparison analysis of invasive cases, normal and AIS uncovered critical genes that involved in the LUAD invasion progression. Furthermore, the GA-based network method revealed gene clusters that may function in the pathways contributing to tumor invasion. The interactions between differentially expressed genes and putative driver genes identified through the network analysis can offer new targets for preventing the cancer invasion and potentially increase the survival rate for cancer patients.14.
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.15.
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.16.
Background
Cellular behaviors are governed by interaction networks among biomolecules, for example gene regulatory and signal transduction networks. An often used dynamic modeling framework for these networks, Boolean modeling, can obtain their attractors (which correspond to cell types and behaviors) and their trajectories from an initial state (e.g. a resting state) to the attractors, for example in response to an external signal. The existing methods however do not elucidate the causal relationships between distant nodes in the network.Results
In this work, we propose a simple logic framework, based on categorizing causal relationships as sufficient or necessary, as a complement to Boolean networks. We identify and explore the properties of complex subnetworks that are distillable into a single logic relationship. We also identify cyclic subnetworks that ensure the stabilization of the state of participating nodes regardless of the rest of the network. We identify the logic backbone of biomolecular networks, consisting of external signals, self-sustaining cyclic subnetworks (stable motifs), and output nodes. Furthermore, we use the logic framework to identify crucial nodes whose override can drive the system from one steady state to another. We apply these techniques to two biological networks: the epithelial-to-mesenchymal transition network corresponding to a developmental process exploited in tumor invasion, and the network of abscisic acid induced stomatal closure in plants. We find interesting subnetworks with logical implications in these networks. Using these subgraphs and motifs, we efficiently reduce both networks to succinct backbone structures.Conclusions
The logic representation identifies the causal relationships between distant nodes and subnetworks. This knowledge can form the basis of network control or used in the reverse engineering of networks.17.
Bing-Qian Su Ying-Qian Han Shuang-Shuang Fan Sheng-Li Ming Bo Wan Wei-Fei Lu Bei-Bei Chu Guo-Yu Yang Jiang Wang 《Biotechnology letters》2018,40(4):641-648
Objective
The purpose of the article is to evaluate the changes in lipid metabolism in bovine mammary-gland epithelial MAC-T cells after PKM2 knockdown.Results
MAC-T cells stably expressing low levels of PKM2 were established with lentivirus-mediated small hairpin RNA. Although the knockdown of PKM2 had no effect on MAC-T cell growth, the reduced expression of PKM2 attenuated the mRNA and protein expression of key enzymes involved in sterol synthesis through the SREBP pathway.Conclusions
The downregulation of PKM2 significantly influenced lipid synthesis in bovine mammary-gland epithelial MAC-T cells. These findings extend our understanding of the crosstalk between glycolysis and lipid metabolism in bovine mammary-gland epithelial cells.18.
Background and aims
Due to the well-known importance of biocrusts for several ecosystem properties linked to soil functionality, we aim to go deeper into the physiological performance of biocrusts components. Possible functional convergences in the physiology of biocrust constituents would facilitate the understanding of both species and genus distributional patterns and improve the possibility of modelling their response to climate change.Methods
We measured gas exchange in the laboratory under controlled conditions of lichen- and moss-dominated biocrusts from four environmentally different locations in Europe. Field data were used to determine the natural hydration sources that drive metabolic activity of biocrusts.Results
Our results show different activity drivers at the four sites. Within site analyses showed similar C fixation for the different crust types in the three sites without hydric stress whilst light use related parameters and respiration at 15 °C were similar in the between sites analyses. There were significant differences in water relations between the biocrusts types, with moss-dominated crusts showing higher maximum and optimum water contents.Conclusions
The functional type approach for biocrusts can be justified from a physiological perspective when similar values are found in the within and between site analyses, the latter indicating habitat independent adaptation patterns. Our multi-site analyses for biocrusts functional performance provide comparisons of C fluxes and water relations in the plant-soil interface that will help to understand the adaptation ability of these communities to possible environmental changes.19.
Clara Pérez-Rambla Leonor Puchades-Carrasco María García-Flores José Rubio-Briones José Antonio López-Guerrero Antonio Pineda-Lucena 《Metabolomics : Official journal of the Metabolomic Society》2017,13(5):52
Introduction
Prostate cancer (PCa) is one of the most common malignancies in men worldwide. Serum prostate specific antigen (PSA) level has been extensively used as a biomarker to detect PCa. However, PSA is not cancer-specific and various non-malignant conditions, including benign prostatic hyperplasia (BPH), can cause a rise in PSA blood levels, thus leading to many false positive results.Objectives
In this study, we evaluated the potential of urinary metabolomic profiling for discriminating PCa from BPH.Methods
Urine samples from 64 PCa patients and 51 individuals diagnosed with BPH were analysed using 1H nuclear magnetic resonance (1H-NMR). Comparative analysis of urinary metabolomic profiles was carried out using multivariate and univariate statistical approaches.Results
The urine metabolomic profile of PCa patients is characterised by increased concentrations of branched-chain amino acids (BCAA), glutamate and pseudouridine, and decreased concentrations of glycine, dimethylglycine, fumarate and 4-imidazole-acetate compared with individuals diagnosed with BPH.Conclusion
PCa patients have a specific urinary metabolomic profile. The results of our study underscore the clinical potential of metabolomic profiling to uncover metabolic changes that could be useful to discriminate PCa from BPH in a clinical context.20.
An efficient algorithm for identifying primary phenotype attractors of a large-scale Boolean network