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1.
Tanushri Chatterji Suruchi Singh Manodeep Sen Ajai Kumar Singh Pradeep Kumar Maurya Nuzhat Husain Janmejai Kumar Srivastava Sudhir Kumar Mandal Raja Roy 《Metabolomics : Official journal of the Metabolomic Society》2016,12(8):130
Introduction
Meningitis, a morbidly infectious central nervous system pathology is accompanied by acute inflammation of the meninges, causing raised intracranial pressure linked with serious neurological sequelae.Objective
To observe the variation in the metabolic profile, that may occur in serum and urine along with CSF in adults using 1H NMR spectroscopy, with an attempt of appropriate and timely treatment regimen.Methods
The 1H NMR-based metabolomics has been performed in 115 adult subjects for differentiating bacterial meningitis (BM) and tubercular meningitis (TBM).Results
The discriminant function analysis (DFA) of the three bio-fluids collectively identified 3-hydroxyisovalerate, lactate, glucose, formate, valine, alanine, ketonic bodies, malonate and choline containing compounds (choline and GPC) as significant metabolites among cases versus control group. The differentiation of bacterial meningitis and tuberculous meningitis (BM vs. TBM) can be done on the basis of identification of 3-hydroxyisovalerate, isobutyrate and formate in case of CSF (with a correct classification of 78 %), alanine in serum (correct classification 60 %), valine and acetone in case of urine (correct classification 89.1 %). The NMR spectral bins based orthogonal signal correction principal component analysis score plots of significant metabolites obtained from DFA also provided group classification among cases versus control group in CSF, serum and urine samples. The variable importance in projection scores also identified similar significant metabolites as obtained from DFA, collectively in CSF, serum and urine samples, responsible for differentiation of meningitis.Conclusion
The CSF contained metabolites which are formed during infection and inflammation, and these were also found in significant quantity in serum and urine samples.2.
3.
Daria V. Dibrova Kirill A. Konovalov Vadim V. Perekhvatov Konstantin V. Skulachev Armen Y. Mulkidjanian 《Biology direct》2017,12(1):29
Background
The Clusters of Orthologous Groups (COGs) of proteins systematize evolutionary related proteins into specific groups with similar functions. However, the available databases do not provide means to assess the extent of similarity between the COGs.Aim
We intended to provide a method for identification and visualization of evolutionary relationships between the COGs, as well as a respective web server.Results
Here we introduce the COGcollator, a web tool for identification of evolutionarily related COGs and their further analysis. We demonstrate the utility of this tool by identifying the COGs that contain distant homologs of (i) the catalytic subunit of bacterial rotary membrane ATP synthases and (ii) the DNA/RNA helicases of the superfamily 1.Reviewers
This article was reviewed by Drs. Igor N. Berezovsky, Igor Zhulin and Yuri Wolf.4.
Xinchang Kou Tongqing Su Ningning Ma Qi Li Peng Wang Zhengfang Wu Wenju Liang Weixin Cheng 《Plant and Soil》2018,422(1-2):129-134
Background
Seeds host bacterial inhabitants but only a limited knowledge is available on which taxa inhabit seed, which niches could be colonized, and what the routes of colonization are.Scope
Within this commentary, a discussion is provided on seed bacterial inhabitants, their taxa, and from where derive the seed colonizers.Conclusions
Seeds/and grains host specific bacteria deriving from the anthosphere, carposphere, or from cones of gymnosperms and inner tissues of plants after a long colonization from the soil to reproductive organs.5.
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.6.
Xijun Liang Zhonghang Xia Xinnan Niu Andrew J Link Liping Pang Fang-Xiang Wu Hongwei Zhang 《Proteome science》2013,11(Z1):S10
Background
The sequence database searching has been the dominant method for peptide identification, in which a large number of peptide spectra generated from LC/MS/MS experiments are searched using a search engine against theoretical fragmentation spectra derived from a protein sequences database or a spectral library. Selecting trustworthy peptide spectrum matches (PSMs) remains a challenge.Results
A novel scoring method named FC-Ranker is developed to assign a nonnegative weight to each target PSM based on the possibility of its being correct. Particularly, the scores of PSMs are updated by using a fuzzy SVM classification model and a fuzzy silhouette index iteratively. Trustworthy PSMs will be assigned high scores when the algorithm stops.Conclusions
Our experimental studies show that FC-Ranker outperforms other post-database search algorithms over a variety of datasets, and it can be extended to solve a general classification problem with uncertain labels.7.
Mohamed Elshikh Syed Ahmed Scott Funston Paul Dunlop Mark McGaw Roger Marchant Ibrahim M. Banat 《Biotechnology letters》2016,38(6):1015-1019
Objectives
To develop and validate a microdilution method for measuring the minimum inhibitory concentration (MIC) of biosurfactants.Results
A standardized microdilution method including resazurin dye has been developed for measuring the MIC of biosurfactants and its validity was established through the replication of tetracycline and gentamicin MIC determination with standard bacterial strains.Conclusion
This new method allows the generation of accurate MIC measurements, whilst overcoming critical issues related to colour and solubility which may interfere with growth measurements for many types of biosurfactant extracts.8.
Connor Black Olivier P. Chevallier Simon A. Haughey Julia Balog Sara Stead Steven D. Pringle Maria V. Riina Francesca Martucci Pier L. Acutis Mike Morris Dimitrios S. Nikolopoulos Zoltan Takats Christopher T. Elliott 《Metabolomics : Official journal of the Metabolomic Society》2017,13(12):153
Introduction
Fish fraud detection is mainly carried out using a genomic profiling approach requiring long and complex sample preparations and assay running times. Rapid evaporative ionisation mass spectrometry (REIMS) can circumvent these issues without sacrificing a loss in the quality of results.Objectives
To demonstrate that REIMS can be used as a fast profiling technique capable of achieving accurate species identification without the need for any sample preparation. Additionally, we wanted to demonstrate that other aspects of fish fraud other than speciation are detectable using REIMS.Methods
478 samples of five different white fish species were subjected to REIMS analysis using an electrosurgical knife. Each sample was cut 8–12 times with each one lasting 3–5 s and chemometric models were generated based on the mass range m/z 600–950 of each sample.Results
The identification of 99 validation samples provided a 98.99% correct classification in which species identification was obtained near-instantaneously (≈?2 s) unlike any other form of food fraud analysis. Significant time comparisons between REIMS and polymerase chain reaction (PCR) were observed when analysing 6 mislabelled samples demonstrating how REIMS can be used as a complimentary technique to detect fish fraud. Additionally, we have demonstrated that the catch method of fish products is capable of detection using REIMS, a concept never previously reported.Conclusions
REIMS has been proven to be an innovative technique to help aid the detection of fish fraud and has the potential to be utilised by fisheries to conduct their own quality control (QC) checks for fast accurate results.9.
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.10.
Background
Non-invasive brain stimulation-related seizures or syncopal events are rare. However, we report on a syncopal event in a healthy female during a transcranial magnetic stimulation single-pulse testing session.Case presentation
A 47-year-old healthy female presented for a transcranial magnetic stimulation session involving single-pulse assessment of cortical excitability. During the session, the participant appeared to have a brief event involving fainting and myoclonic jerks of the upper extremities. Orthostatic assessment was performed after the event and physician evaluation determined that this was a vasovagal syncopal event. The ethical aspects of this neurophysiology testing protocol were reviewed by the University of Minnesota Institutional Review Board (IRB), and formal IRB approval was deemed unnecessary for single-pulse assessment of healthy control participants not directly involved in a research study. Informed consent was obtained by the participant, including review of potential adverse events.Conclusion
Although rare and rarely reported, vasovagal syncopal events surrounding non-invasive brain stimulation do occur. Thorough pre-screening should incorporate assessment of history of syncope and a plan for risk mitigation if such an event should occur. A complete assessment of the impact of stimulation on the autonomic nervous system is unknown. As such studies expand into patients with myriad neurologic diagnoses, further studies on this effect, in both healthy control and patient populations, are warranted. Such knowledge could contribute to identification of the optimal study participant, and improvements in techniques of stimulation administration.Keywords
Non-invasive brain stimulation, Transcranial magnetic stimulation, Vasovagal syncope, Adverse events11.
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.12.
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.13.
Robert M Kirby Abdul Basit Quang T Nguyen Anthony Jaipersad Rebecca Billingham 《International Seminars in Surgical Oncology : ISSO》2007,4(1):30
Aims
This paper describes a simple technique of axillary and breast massage which improves the successful identification of blue sentinel nodes using patent blue dye alone.Methods
Patent blue dye was injected in the subdermal part of the retroaroelar area in 167 patients having surgical treatment for invasive breast cancer. Three stage axillary lymphatic massage was performed prior to making the axillary incision for sentinel lymph node biopsy. All patients had completion axillary sampling or clearance.Results
A blue lymphatic duct leading to lymph nodes of the first drainage was identified in 163 (97%) of the patients. Results are compared with 168 patients who had sentinel lymph node biopsy using blue dye without axillary massage. Allergic reactions were observed in four patients (1.2%).Conclusion
Three stage axillary lymphatic massage improves the successful identification of a blue sentinel lymph node in breast cancer patients.14.
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.15.
Yingfeng Wang Xutao Wang Xiaoqin Zeng 《Metabolomics : Official journal of the Metabolomic Society》2017,13(10):116
Introduction
Tandem mass spectrometry (MS/MS) has been widely used for identifying metabolites in many areas. However, computationally identifying metabolites from MS/MS data is challenging due to the unknown of fragmentation rules, which determine the precedence of chemical bond dissociation. Although this problem has been tackled by different ways, the lack of computational tools to flexibly represent adjacent structures of chemical bonds is still a long-term bottleneck for studying fragmentation rules.Objectives
This study aimed to develop computational methods for investigating fragmentation rules by analyzing annotated MS/MS data.Methods
We implemented a computational platform, MIDAS-G, for investigating fragmentation rules. MIDAS-G processes a metabolite as a simple graph and uses graph grammars to recognize specific chemical bonds and their adjacent structures. We can apply MIDAS-G to investigate fragmentation rules by adjusting bond weights in the scoring model of the metabolite identification tool and comparing metabolite identification performances.Results
We used MIDAS-G to investigate four bond types on real annotated MS/MS data in experiments. The experimental results matched data collected from wet labs and literature. The effectiveness of MIDAS-G was confirmed.Conclusion
We developed a computational platform for investigating fragmentation rules of tandem mass spectrometry. This platform is freely available for download.16.
Ling Bai Wei He Tianpeng Li Cuiting Yang Yingping Zhuang Shu Quan 《Biotechnology letters》2017,39(8):1191-1199
Objective
To investigate the application of the TEM-1 β-lactamase protein fragment complementation assay (PCA) in detecting weak and unstable protein–protein interactions as typically observed during chaperone-assisted protein folding in the periplasm of Escherichia coli.Results
The TEM-1 β-lactamase PCA system effectively captured the interactions of three pairs of chaperones and substrates. Moreover, the strength of the interactions can be quantitatively analyzed by comparing different levels of penicillin resistance, and the assay can be performed under 0.5% butanol, a stress condition thought to be physiologically relevant.Conclusions
The β-lactamase PCA system faithfully reports chaperone-substrate interactions in the bacterial cell envelope, and therefore this system has the potential to map the complex protein homeostasis network under a fluctuating environment.17.
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.18.
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.19.
Daniel Cañueto Josep Gómez Reza M. Salek Xavier Correig Nicolau Cañellas 《Metabolomics : Official journal of the Metabolomic Society》2018,14(3):24
Introduction
Adoption of automatic profiling tools for 1H-NMR-based metabolomic studies still lags behind other approaches in the absence of the flexibility and interactivity necessary to adapt to the properties of study data sets of complex matrices.Objectives
To provide an open source tool that fully integrates these needs and enables the reproducibility of the profiling process.Methods
rDolphin incorporates novel techniques to optimize exploratory analysis, metabolite identification, and validation of profiling output quality.Results
The information and quality achieved in two public datasets of complex matrices are maximized.Conclusion
rDolphin is an open-source R package (http://github.com/danielcanueto/rDolphin) able to provide the best balance between accuracy, reproducibility and ease of use.20.
Dorothea Lesche Roland Geyer Daniel Lienhard Christos T. Nakas Gaëlle Diserens Peter Vermathen Alexander B. Leichtle 《Metabolomics : Official journal of the Metabolomic Society》2016,12(10):159