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1.
J Agric Food Chem ; 67(38): 10614-10623, 2019 Sep 25.
Artigo em Inglês | MEDLINE | ID: mdl-31483658

RESUMO

Type 2 diabetes (T2D) is a pandemic disease chiefly characterized by hyperglycemia. In this study, the combination of serum lipidomic and metabolomic approach was employed to investigate the effect of arabinoxylan on type 2 diabetic rats and identify the critical biomarkers of T2D. Metabolomics analysis revealed that branched-chain amino acids, 12α-hydroxylated bile acids, ketone bodies, and several short- and long-chain acylcarnitines were significantly increased in T2D, whereas lysophosphatidylcholines (LPCs) were significantly decreased. Lipidomics analysis indicated T2D-related dyslipidemia was mainly associated with the increased levels of acetylcarnitine, free fatty acids (FFA), diacylglycerols, triacylglycerols, and cholesteryl esters and the decreased levels of some unsaturated phosphatidylcholines (less than 22 carbons). These variations indicated the disturbed amino acid and lipid metabolism in T2D, and the accumulation of incompletely oxidized lipid species might eventually contribute to impaired insulin action and glucose homeostasis. Arabinoxylan treatment decreased the concentrations of 12α-hydroxylated bile acids, carnitines, and FFAs and increased the levels of LPCs. The improved bile acid and lipid metabolism by arabinoxylan might be involved in the alleviation of hypercholesterolemia and hyperlipidemia in T2D.


Assuntos
Anticolesterolemiantes/administração & dosagem , Diabetes Mellitus Tipo 2/tratamento farmacológico , Hipercolesterolemia/tratamento farmacológico , Hiperlipidemias/tratamento farmacológico , Hipoglicemiantes/administração & dosagem , Hipolipemiantes/administração & dosagem , Xilanos/administração & dosagem , Aminoácidos de Cadeia Ramificada/metabolismo , Animais , Ácidos e Sais Biliares/metabolismo , Carnitina/metabolismo , Diabetes Mellitus Tipo 2/complicações , Diabetes Mellitus Tipo 2/metabolismo , Ácidos Graxos não Esterificados/metabolismo , Glucose/metabolismo , Humanos , Hipercolesterolemia/etiologia , Hipercolesterolemia/metabolismo , Hiperlipidemias/etiologia , Hiperlipidemias/metabolismo , Metabolismo dos Lipídeos , Lipídeos/química , Metabolômica , Ratos
2.
Zhongguo Dang Dai Er Ke Za Zhi ; 21(9): 942-948, 2019 Sep.
Artigo em Chinês | MEDLINE | ID: mdl-31506158

RESUMO

Metabolomics is an emerging and popular subject in the post-genome era, and a large number of studies have been noted on the application of metabolomics in health evaluation, growth and development evaluation, disease diagnosis, and therapeutic efficacy evaluation. As a special period of life, the neonatal period is characterized by rapid cell renewing, consumption of a lot of energy and materials, and changes in metabolic pathways, all of which affect the level of metabolites. However, there is still no reference standard for metabolic level and profile in neonates. This article reviews the current status of metabolic research on neonatal growth and development and common diseases and related clinical application of metabolomics, so as to provide new ideas for nutrition guidance and evaluation, selection of therapeutic regimens, and new drug research in neonates.


Assuntos
Redes e Vias Metabólicas , Metabolômica , Humanos , Recém-Nascido
3.
Adv Exp Med Biol ; 1161: 101-113, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31562625

RESUMO

The treatment of psychiatric disorders remains a significant challenge in part due to imprecise diagnostic criteria and incomplete understanding of the molecular pathology involved. Current diagnostic and pharmacological treatment guidelines use a uniform approach to address each disorder even though psychiatric clinical presentation and prognosis within a disorder are known to be heterogeneous. Limited therapeutic success highlights the need for a precision medicine approach in psychiatry, termed precision psychiatry. To practice precision psychiatry, it is essential to research and develop multiple omics-based biomarkers that consider environmental factors and careful phenotype determination. Metabolomics, which lies at the endpoint of the "omics cascade," allows for detection of alterations in systems-level metabolites within biological pathways, thereby providing insights into the mechanisms that underlie various physiological conditions and pathologies. The eicosanoids, a family of metabolites derived from oxygenated polyunsaturated fatty acids, play a key role in inflammatory mechanisms and have been implicated in psychiatric disorders such as anorexia nervosa and depression. This review (1) provides background on the current clinical challenges of psychiatric disorders, (2) gives an overview of metabolomics application as a tool to develop improved biomarkers for precision psychiatry, and (3) summarizes current knowledge on metabolomics and lipidomic findings in common psychiatric disorders, with a focus on eicosanoids. Metabolomics is a promising tool for precision psychiatry. This research has great potential for both discovering biomarkers and elucidating molecular mechanisms underlying psychiatric disorders.


Assuntos
Biomarcadores , Transtornos Mentais , Medicina de Precisão , Psiquiatria , Humanos , Transtornos Mentais/sangue , Transtornos Mentais/fisiopatologia , Metabolômica
4.
Yi Chuan ; 41(9): 883-892, 2019 Sep 20.
Artigo em Chinês | MEDLINE | ID: mdl-31549686

RESUMO

Metabolomics (defined as comprehensive small molecule chemical analysis), together with genomics, transcriptomics, proteomics and phenomics, now plays a fundamental role in system biological studies. Chromatography- mass spectrometry machines, which have the characteristics of high resolution and high sensitivity, are widely used for metabolomics analysis, both qualitatively and quantitatively. With the fast development of the chromatography-mass spectrometry technology, metabolomics analysis has been successfully applied in various biological research fields. Here, we introduce the different chromatography-mass spectrum machines used for metabolomics analysis and their applications to various biological issues by mainly using the metabolomics platform in Institute of Genetics and Developmental Biology as a case study.


Assuntos
Metabolômica/instrumentação , Metabolômica/tendências , Cromatografia , Genômica , Espectrometria de Massas , Proteômica
5.
Plant Dis ; 103(10): 2541-2547, 2019 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-31432772

RESUMO

To prevent the spread of anthracnose in strawberry plants and characterize the metabolic changes occurring during plant-pathogen interactions, we developed a method for the early diagnosis of disease based on an analysis of the metabolome by gas chromatography-mass spectrometry. An examination of the metabolic profile revealed 189 and 202 total ion chromatogram peaks for the control and inoculated plants, respectively. A partial least squares discriminant analysis (PLS-DA) model was conducted for the reliable and accurate discrimination between healthy and diseased strawberry plants, even in the absence of disease symptoms (e.g., early stages of infection). ANOVA (analysis of variance) and orthogonal partial least squares analysis (OPLS) identified 20 metabolites as tentative biomarkers of Colletotrichum theobromicola infection (e.g., citric acid, d-xylose, erythrose, galactose, gallic acid, malic acid, methyl α-galactopyranoside, phosphate, and shikimic acid). At least some of these potential biomarkers may be applicable for the early diagnosis of anthracnose in strawberry plants. Moreover, these metabolites may be useful for characterizing pathogen infections and plant defense responses. This study confirms the utility of metabolomics research for developing diagnostic tools and clarifying the mechanism underlying plant-pathogen interactions. Furthermore, the data presented herein may be relevant for developing new methods for preventing anthracnose in strawberry seedlings cultivated under field conditions.


Assuntos
Biomarcadores , Colletotrichum , Fragaria , Cromatografia Gasosa-Espectrometria de Massas , Metabolômica , Biomarcadores/análise , Colletotrichum/fisiologia , Fragaria/microbiologia
6.
Bioresour Technol ; 291: 121890, 2019 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-31378447

RESUMO

In recent impetus of phycological research, microalgae have emerged as a potential candidate for various arena of application-driven research. Omics-based tactics are used for disentangling the regulation and network integration for biosynthesis/degradation of metabolic precursors, intermediates, end products, and identifying the networks that regulate the metabolic flux. Multi-omics coupled with data analytics have facilitated understanding of biological processes and allow ample access to diverse metabolic pathways utilized for genetic manipulations making microalgal factories more efficient. The present review discusses state-of-art "Algomics" and the prospect of microalgae and their role in symbiotic association by using omics approaches including genomics, transcriptomics, proteomics and metabolomics. Microalgal based uni- and multi-omics approaches are critically analyzed in wastewater treatment, metal toxicity and remediation, biofuel production, and therapeutics to provide an imminent outlook for an array of environmentally sustainable and economically viable microalgal applications.


Assuntos
Microalgas/metabolismo , Animais , Genômica/métodos , Humanos , Metabolômica , Proteômica , Águas Residuárias/química
7.
Bioresour Technol ; 292: 122002, 2019 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-31437797

RESUMO

The major goal of this study was to explore the functions of butylated hydroxyanisole (BHA) combined with abiotic stress on the cultivation of the microalga Haematococcus pluvialis for astaxanthin and lipid production. Here, the effect of BHA on astaxanthin and lipid accumulation and physiological and metabolomic profiles was investigated. These results suggested that astaxanthin content was increased by 2.17-fold compared to the control. The lipid content was enhanced by 1.22-fold. BHA treatment simultaneously reduced carbohydrates and protein and delayed the decay of chlorophyll. Furthermore, metabolomic analysis demonstrated that BHA upregulated and activated the bioprocesses involved in cellular basal metabolism and signalling systems, such as glycolysis, the TCA cycle, amino acid metabolism and the phosphatidylinositol signalling system, thus enhancing astaxanthin and lipid accumulation. Altogether, this research shows the dramatic effects of BHA on algal metabolism in the regulation of key metabolic nodes and provides novel insights into microalgal regulation and metabolism.


Assuntos
Hidroxianisol Butilado , Lipídeos , Metabolômica , Xantofilas
8.
J Agric Food Chem ; 67(35): 9967-9978, 2019 Sep 04.
Artigo em Inglês | MEDLINE | ID: mdl-31403784

RESUMO

Following the recent completion of the draft genome sequence of the tea plant, high-throughput decoding of gene function, especially for those involved in complex secondary metabolic pathways, has become a major challenge. Here, we profiled the metabolome and transcriptome of 11 tea cultivars, and then illustrated a weighted gene coexpression network analysis (WGCNA)-based system biological strategy to interpret metabolomic flux, predict gene functions, and mine key regulators involved in the flavonoid biosynthesis pathway. We constructed a multilayered regulatory network, which integrated the gene coexpression relationship with the microRNA target and promoter cis-regulatory element information. This allowed us to reveal new uncharacterized TFs (e.g., MADSs, WRKYs, and SBPs) and microRNAs (including 17 conserved and 15 novel microRNAs) that are potentially implicated in different steps of the catechin biosynthesis. Furthermore, we applied metabolic-signature-based association method to capture additional key regulators involved in catechin pathway. This provides important clues for the functional characterization of five SCPL1A acyltransferase family members, which might be implicated in the production balance of anthocyanins, galloylated catechins, and proanthocyanins. Application of an "omics"-based system biology strategy should facilitate germplasm utilization and provide valuable resources for tea quality improvement.


Assuntos
Camellia sinensis/metabolismo , Flavonoides/química , Redes Reguladoras de Genes , Camellia sinensis/química , Camellia sinensis/classificação , Camellia sinensis/genética , Flavonoides/metabolismo , Regulação da Expressão Gênica de Plantas , Metabolômica , Folhas de Planta/química , Folhas de Planta/classificação , Folhas de Planta/genética , Folhas de Planta/metabolismo , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo , Transcriptoma
9.
Food Chem ; 300: 125169, 2019 Dec 01.
Artigo em Inglês | MEDLINE | ID: mdl-31336273

RESUMO

Red drupelet is a postharvest disorder of blackberries with several drupelets turning back to red. This affects visual quality and thus marketability and consumers' acceptance. However, the cause of this disorder as well as metabolite changes during color reversion have not been fully understood. Anthocyanins, cyanidin 3-glucoside, cyanidin 3-malonylglucoside, cyanidin 3-dioxalylglucoside, and total anthocyanin, were significantly lower in red drupelets than in black drupelets after 7 days of storage. Sugars and organic acids, lipids, and free amino acids also changed with storage and by color reversion. The untargeted metabolomics analyses indicated that red drupelets were generally differentiated from berries at harvest or black drupelets at metabolite level. The results of this study help better understand the red drupelet disorder. To our knowledge, this is the first study investigating red drupelet disorder by comparing black and red drupelets at metabolite level.


Assuntos
Metabolômica/métodos , Rubus/metabolismo , Aminoácidos/análise , Aminoácidos/metabolismo , Antocianinas/análise , Antocianinas/metabolismo , Cor , Qualidade dos Alimentos , Armazenamento de Alimentos , Frutas/química , Glucosídeos/análise , Glucosídeos/metabolismo , Lipídeos/análise , Rubus/química
10.
Adv Exp Med Biol ; 1140: 613-633, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31347075

RESUMO

Recently, metabolomics-the study of metabolite profiles within biological samples-has found a wide range of applications. This chapter describes the different techniques available for metabolomic analysis, the various samples that can be utilised for analysis and applications of both global and targeted metabolomic analysis to biomarker discovery in medicine.


Assuntos
Biomarcadores , Pesquisa Biomédica , Metabolômica , Humanos
11.
Adv Exp Med Biol ; 1140: 635-647, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31347076

RESUMO

The advancement of mass spectrometry-based analytical platform largely facilitates small-molecule metabolomics studies, which allows simultaneously analysis of a large number of metabolites from bio-samples and give a general picture of metabolic changes related to diseases or environmental alteration. Due to the large diversity of cellular metabolites, globally and precisely examining metabolic profile remains the most challenging part in metabolomic experiment. Mass spectrometry coupled with liquid chromatography enhances sensitivity and resolving power of metabolites identification and quantification, as well as versatility of analyzing a wide array of metabolites. In this chapter, we discussed the technical aspects of each step in the workflow of metabolomics studies we aimed to give technical guidelines for metabolomics investigation design and approach.


Assuntos
Espectrometria de Massas , Metaboloma , Metabolômica , Cromatografia Líquida
12.
Adv Exp Med Biol ; 1140: 771-785, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31347084

RESUMO

Mass spectrometry (MS) is a powerful technique that has various applications including the identification and characterization of proteins, protein-protein interactions and protein post translational modifications, as well as other molecules (i.e. metabolites, lipids, nucleotides and polynucleotides). However, not too many undergraduate students within the USA and around the world have access to (and are trained in) MS. The undergraduate students in our department are taught to analyze proteomics and metabolomics data obtained from MS analysis, including de novo sequencing of peptides and to interpret the MS and MS/MS data acquired in positive and negative ionization modes. Here, we give some examples of MS data analyzed in the Biochemistry I class and then examples of some independent research projects performed by students over the years in the Biochemistry and Biotechnology laboratory, where MS is used for both proteins, peptides and metabolites analysis, thus demonstrating the applicability of MS analysis in diverse fields. The projects discussed include analysis of the protein content present in yogurt, beer, protein shakes, contact lenses, or milk of animal or vegetal origin.


Assuntos
Metabolômica , Proteômica , Espectrometria de Massas em Tandem , Universidades , Animais , Humanos , Peptídeos , Proteínas
13.
Zhongguo Zhong Yao Za Zhi ; 44(10): 2139-2148, 2019 May.
Artigo em Chinês | MEDLINE | ID: mdl-31355573

RESUMO

In this paper,ultra performance liquid chromatography coupled with time-of-flight mass spectrometry( UPLC-Q-TOFMS) technique was used to study the effects of steamed notoginseng on endogenous markers in plasma of rats with hemolytic anemia induced by N-acetyl phenyl hydrazine( APH). The aim was to find out the potential biomarkers and possible blood enriching mechanism of steamed notoginseng on hemolytic anemia rats. In the experiment,steamed notoginseng medicine pair( steamed notoginseng-ginseng)and compound medicines( Sanqi Yangxue Capsules) were used respectively to intervene in APH-induced hemolytic anemia model rats.Then blood routine indexes such as red blood cells( RBC),hemoglobin( Hb) and related organ indexes were determined. As compared with the blank group,the RBC and Hb levels in the model group were substantially decreased( P< 0. 01),while the liver and spleen organ indexes were increased( P< 0. 05). The results of blood routine and organ index demonstrated that the blood deficiency model was successfully established. Steamed notoginseng can significantly increase the RBC level of rats( P<0. 01),and the related indicators of each drug group had a trend of returning to normal levels,verifying the blood enriching effect of steamed notoginseng. The UPLC-Q-TOF-MS technique,principal component analysis( PCA) and partial least squares-discrimination analysis( PLS-DA) were used to analyze the metabolic profiles between the normal group and the model group. Twenty-six potential biomarkers for hemolytic anemia were screened in plasma. Nine metabolites such as retinol,L-valine,and arachidonic acid were down-regulated in the blood deficiency rats,and 17 metabolites such as protoporphyrin Ⅸ and niacinamide were up-regulated. The metabolic level of biomarkers could be changed to a normal state after rats were given with steamed notoginseng,drug pairs,and compound prescriptions. It can be speculated that steamed notoginseng may play a role of blood tonifying by improving biosynthesis of valine,leucine and isoleucine,as well as metabolic pathways such as retinol metabolism and arachidonic acid metabolism.


Assuntos
Anemia Hemolítica/tratamento farmacológico , Medicamentos de Ervas Chinesas/farmacologia , Metabolômica , Panax notoginseng/química , Animais , Biomarcadores , Espectrometria de Massas , Metaboloma , Ratos , Vapor
14.
J Agric Food Chem ; 67(32): 8773-8782, 2019 Aug 14.
Artigo em Inglês | MEDLINE | ID: mdl-31283205

RESUMO

Conquering rapid postripeness and deterioration of Agaricus bisporus is quite challenging. We previously observed that methyl jasmonate (MeJA) pretreatment postponed the deterioration of A. bisporus, but the mechanism is unknown. Here, a nontargeted metabolomics analysis by ultrahigh-pressure liquid chromatography-quadrupole-time-of-flight tandem mass spectrometry (UHPLC-QTOF-MS/MS) revealed that MeJA increased the synthesis of malate by inhibiting the decomposition of fumarate and cis-aconitate. MeJA maintained energy supply by enhancing ATP content and energy charge level and improving hexokinase and glucose-6-phosphate dehydrogenase activities as well. These results promoted ATP supply by maintaining glycolysis, the TCA cycle, and the pentose phosphate pathway. In addition, we revealed that the delayed deterioration was attributed to MeJA treatment which stimulated the energy status of A. bisporus by reducing the respiration rate and nutrient decomposition, thus maintaining energy production. Our results provide a new insight into the role of MeJA treatment in delaying deterioration of A. bisporus through ATP production and supply.


Assuntos
Acetatos/farmacologia , Agaricus/efeitos dos fármacos , Agaricus/metabolismo , Ciclopentanos/farmacologia , Oxilipinas/farmacologia , Ácido Aconítico/metabolismo , Trifosfato de Adenosina/metabolismo , Agaricus/química , Agaricus/crescimento & desenvolvimento , Cromatografia Líquida de Alta Pressão/métodos , Metabolismo Energético/efeitos dos fármacos , Fumaratos/metabolismo , Malatos/metabolismo , Metabolômica , Espectrometria de Massas em Tandem/métodos
15.
Anal Bioanal Chem ; 411(20): 5089-5098, 2019 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-31278548

RESUMO

A confounding factor is an unstudied factor that affects one or more of the variables that are being studied in an investigation, so the presence of a confounder may lead to inaccurate or biased results. It is well recognized that physiological and environmental factors such as race, diet, age, gender, blood pressure, and diurnal cycle affect mammalian metabolism. To eliminate the noise introduced by confounders into metabolomics studies, a GUI-based method denoted metabolic confounding effect elimination (MCEE) was developed and has since been applied successfully in a wide range of metabolomics studies. To keep up with recent developments in computational metabolomics and a growing number of user requests, an upgraded version of MCEE with more options and enhanced performance was designed and developed. Besides the generalized linear model (GLM) method, a multivariate method for selecting affected metabolites-canonical correlation analysis (CCA)-was introduced, which accounts for complicated correlations and collinearity within the metabolome. Multiple confounders are acceptable and can be identified and processed separately or simultaneously. The effectiveness of this new version of MCEE as well as the pros and cons of the two methodological options were examined using three simulated data sets (a basic model, a model with different sample size ratios, and a sparse model) and two real-world data sets (a human type 2 diabetes mellitus data set and a human arthritis data set). As well as presenting the results of this examination of the new version of MCEE, some instructions on appropriate method selection and parameter setting are provided here. The freely available MATLAB code for MCEE with a GUI has also been updated accordingly at https://github.com/chentianlu/MCEE-2.0 . Graphical abstract.


Assuntos
Metabolômica , Adulto , Fatores Etários , Pressão Sanguínea , Ritmo Circadiano , Feminino , Humanos , Masculino , Pessoa de Meia-Idade
16.
BMC Plant Biol ; 19(1): 289, 2019 Jul 01.
Artigo em Inglês | MEDLINE | ID: mdl-31262259

RESUMO

BACKGROUND: Banana anthracnose, caused by Colletotrichum musae, is one of the most severe postharvest diseases in banana. Melatonin is widely known for its role in enhancing plant stress tolerance. However, little is known about the control of melatonin on anthracnose in postharvest banana fruit. RESULTS: In this study, exogenous melatonin treatment could significantly reduce the incidence of anthracnose in ripe yellow banana fruit and delay fruit senescence. However, melatonin treatment did not affect the growth of Colletotrichum musae in vitro. Transcriptomic analysis of banana peel showed that 339 genes were up-regulated and 241 were down-regulated in the peel after melatonin treatment, compared with the control. Based on GO terms and KEGG pathway, these up-regulated genes were mainly categorized into signal transduction, cell wall formation, secondary metabolism, volatile compounds synthesis and response to stress, which might be related to the anti-anthracnose of banana fruit induced by melatonin treatment. This view was also supported by the increase of volatile compounds, cell wall components and IAA content in the melatonin-treated fruit peel via the metabolomic analysis. After melatonin treatment, auxin, ethylene and mitogen-activated protein kinase (MAPK) signaling pathways were enhanced, which might be involved in the enhanced fruit resistance by regulating physiological characteristics, disease-resistant proteins and metabolites. CONCLUSIONS: Our results provide a better understanding of the molecular processes in melatonin treatment delaying banana fruit senescence and anthracnose incidence.


Assuntos
Colletotrichum/fisiologia , Genes de Plantas , Melatonina/metabolismo , Metaboloma , Musa/microbiologia , Doenças das Plantas/microbiologia , Transcriptoma , Colletotrichum/efeitos dos fármacos , Frutas/microbiologia , Perfilação da Expressão Gênica , Melatonina/administração & dosagem , Metabolômica , Musa/genética
17.
J Agric Food Chem ; 67(30): 8319-8331, 2019 Jul 31.
Artigo em Inglês | MEDLINE | ID: mdl-31287308

RESUMO

The layer of cuticular wax covering fruits plays important roles in protecting against disease, preventing non-stomatal water loss, and extending shelf life. However, the molecular basis of cuticular wax biosynthesis in pear (Pyrus) fruits remains elusive. Our study thoroughly investigates cuticular wax biosynthesis during pear fruit development from morphologic, transcriptomic, and gas chromatography-mass spectrometry metabolomic perspectives. Our results showed that cuticular wax concentrations increased during the early stage [20-80 days after full bloom (DAFB)] from 0.64 mg/cm2 (50 DAFB) to 1.75 mg/cm2 (80 DAFB) and then slightly decreased to 1.22 mg/cm2 during the fruit ripening period (80-140 DAFB). Scanning electron microscopy imaging indicated that wax plate crystals increased and wax structures varied during the pear fruit development. The combined transcriptomic and metabolomic profiling analysis revealed 27 genes, including 12 genes encoding transcription factors and a new structural gene (Pbr028523) encoding ß-amyrin synthase, participating in the biosynthesis, transport, and regulation of cuticular wax according to their expression patterns in pear fruit. The quantitative real-time polymerase chain reaction experiments of 18 differentially expressed genes were performed and confirmed the accuracy of the RNA-Seq-derived transcript expression. A model of VLCFAs and cuticular wax synthesis and transport in pear fruit is proposed, providing a mechanistic framework for understanding cuticular wax biosynthesis in pear fruit. These results and data sets provide a foundation for the molecular events related to cuticular wax in 'Yuluxiang' pear fruit and may also help guide the functional analyses of candidate genes important for improving the cuticular wax of pear fruit in the future.


Assuntos
Epiderme/metabolismo , Frutas/crescimento & desenvolvimento , Pyrus/genética , Ceras/metabolismo , Epiderme/química , Frutas/química , Frutas/genética , Frutas/metabolismo , Cromatografia Gasosa-Espectrometria de Massas , Regulação da Expressão Gênica de Plantas , Metabolômica , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo , Pyrus/química , Pyrus/crescimento & desenvolvimento , Pyrus/metabolismo , Transcriptoma
18.
BMC Bioinformatics ; 20(1): 368, 2019 Jul 01.
Artigo em Inglês | MEDLINE | ID: mdl-31262247

RESUMO

BACKGROUND: Mass Spectrometry (MS) is a widely used technique in biology research, and has become key in proteomics and metabolomics analyses. As a result, the amount of MS data has significantly increased in recent years. For example, the MS repository MassIVE contains more than 123TB of data. Somehow surprisingly, these data are stored uncompressed, hence incurring a significant storage cost. Efficient representation of these data is therefore paramount to lessen the burden of storage and facilitate its dissemination. RESULTS: We present MassComp, a lossless compressor optimized for the numerical (m/z)-intensity pairs that account for most of the MS data. We tested MassComp on several MS data and show that it delivers on average a 46% reduction on the size of the numerical data, and up to 89%. These results correspond to an average improvement of more than 27% when compared to the general compressor gzip and of 40% when compared to the state-of-the-art numerical compressor FPC. When tested on entire files retrieved from the MassIVE repository, MassComp achieves on average a 59% size reduction. MassComp is written in C++ and freely available at https://github.com/iochoa/MassComp . CONCLUSIONS: The compression performance of MassComp demonstrates its potential to significantly reduce the footprint of MS data, and shows the benefits of designing specialized compression algorithms tailored to MS data. MassComp is an addition to the family of omics compression algorithms designed to lessen the storage burden and facilitate the exchange and dissemination of omics data.


Assuntos
Compressão de Dados/métodos , Espectrometria de Massas , Algoritmos , Metabolômica , Proteômica
19.
Zhongguo Zhong Yao Za Zhi ; 44(9): 1760-1766, 2019 May.
Artigo em Chinês | MEDLINE | ID: mdl-31342699

RESUMO

Lipids have been documented to play comprehensive and significant role in many biological processes. As a branch of metabolomics,lipidomics research mainly involves the analysis of the variation of lipid metabolism profiles under different physiologic,pathologic conditions or drug intervention,the discovery of key lipid biomarkers of a disease in lipid metabolic networks,and the study of the mechanism of action of lipid metabolic regulation during disease onset and progression,and drug treatment. Traditional Chinese medicines( TCMs)are characterized with integrated effects by multi-components,multi-targets and integrated effects. It is urgent to develop methods suitable for the study of complex TCMs to reveal the active constituents and integrated mechanism of action. Systems biology such as lipidomics provides valuable strategy and approach to illustrate the complex mechanisms of TCMs. In this paper,in order to provide technical references for TCMs,we have reviewed the analytical techniques applied in lipidomics and the applications of lipidomics in TCMs researches.


Assuntos
Metabolismo dos Lipídeos , Medicina Tradicional Chinesa , Metabolômica/métodos , Biomarcadores
20.
Zhongguo Zhong Yao Za Zhi ; 44(9): 1921-1926, 2019 May.
Artigo em Chinês | MEDLINE | ID: mdl-31342722

RESUMO

In the present study,non-targeted metabolomics technique was used to screen potentially susceptibility biomarkers in patients with mild liver function abnormalities during long-term use of Chinese herbal compound. According to the inclusion and exclusion criteria,we collected 7 cases of patients with abnormal liver function during the period of complete taking Chinese herbal medicine( 60 days),and 18 cases of patients with normal liver function in re-examination from the reproductive medicine center in our hospital. Ultra performance liquid chromatography coupled with time-of-flight mass spectrometry( UPLC-Q-TOF/MS~E) technique combined with Progenesis QI software was used to analyze the differential biomarkers in serum of patients with wild liver function abnormalities and normal liver function. 11 potential biomarkers such as bilirubin,pantothenic acid,hippuric acid,sphingomyelin,palmitic acid,and oleic acid were tentatively identified. Metabolic disorders in patients with herbal-induced mild liver abnormality were mainly related to two pathways: pantothenic acid and coenzyme A biosynthesis and linoleic acid metabolism. It could provide a reference for the early warning of mild liver function abnormalities of patients that may be caused by long-term use of Chinese medicine compound in clinical application,and will lay a foundation for further understanding the endogenous substance changes in different levels of liver injury.


Assuntos
Medicamentos de Ervas Chinesas/efeitos adversos , Hepatopatias/sangue , Metabolômica , Biomarcadores/sangue , Cromatografia Líquida de Alta Pressão , Medicamentos de Ervas Chinesas/uso terapêutico , Humanos , Espectrometria de Massas
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