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Sample records for complementary transcriptomic lipidomic

  1. Lipidomic and Transcriptomic Basis of Lysosomal Dysfunction in Progranulin Deficiency

    Directory of Open Access Journals (Sweden)

    Bret M. Evers

    2017-09-01

    Full Text Available Defective lysosomal function defines many neurodegenerative diseases, such as neuronal ceroid lipofuscinoses (NCL and Niemann-Pick type C (NPC, and is implicated in Alzheimer’s disease (AD and frontotemporal lobar degeneration (FTLD-TDP with progranulin (PGRN deficiency. Here, we show that PGRN is involved in lysosomal homeostasis and lipid metabolism. PGRN deficiency alters lysosome abundance and morphology in mouse neurons. Using an unbiased lipidomic approach, we found that brain lipid composition in humans and mice with PGRN deficiency shows disease-specific differences that distinguish them from normal and other pathologic groups. PGRN loss leads to an accumulation of polyunsaturated triacylglycerides, as well as a reduction of diacylglycerides and phosphatidylserines in fibroblast and enriched lysosome lipidomes. Transcriptomic analysis of PGRN-deficient mouse brains revealed distinct expression patterns of lysosomal, immune-related, and lipid metabolic genes. These findings have implications for the pathogenesis of FTLD-TDP due to PGRN deficiency and suggest lysosomal dysfunction as an underlying mechanism.

  2. Effects of Elaidic Acid on Lipid Metabolism in HepG2 Cells, Investigated by an Integrated Approach of Lipidomics, Transcriptomics and Proteomics

    DEFF Research Database (Denmark)

    Vendel Nielsen, Lone; Hansen, Toke Peter Krogager; Young, Clifford

    2013-01-01

    in a combined proteomic, transcriptomic and lipidomic approach. We found many of the proteins responsible for cholesterol synthesis up-regulated together with several proteins involved in the esterification and hepatic import/export of cholesterol. Furthermore, a profound remodeling of the cellular membrane...... occurred at the phospholipid level. Our findings contribute to the explanation on how trans fatty acids from the diet can cause modifications in plasma cholesterol levels by inducing abundance changes in several hepatic proteins and the hepatic membrane composition....

  3. Harmonizing Lipidomics

    DEFF Research Database (Denmark)

    Bowden, John A; Heckert, Alan; Ulmer, Candice Z

    2017-01-01

    As the lipidomics field continues to advance, self-evaluation within the community is critical. Here, we performed an interlaboratory comparison exercise for lipidomics using Standard Reference Material (SRM) 1950 Metabolites in Frozen Human Plasma, a commercially available reference material. Th...

  4. Transcriptome

    Science.gov (United States)

    ... Also: Talking Glossary of Genetic Terms Definitions for genetic terms used on this page En Español: Transcriptoma Transcriptome What is a transcriptome? What can a transcriptome tell us? How can transcriptome data be used to explore gene function? What is ...

  5. Computational Lipidomics and Lipid Bioinformatics: Filling In the Blanks.

    Science.gov (United States)

    Pauling, Josch; Klipp, Edda

    2016-12-22

    Lipids are highly diverse metabolites of pronounced importance in health and disease. While metabolomics is a broad field under the omics umbrella that may also relate to lipids, lipidomics is an emerging field which specializes in the identification, quantification and functional interpretation of complex lipidomes. Today, it is possible to identify and distinguish lipids in a high-resolution, high-throughput manner and simultaneously with a lot of structural detail. However, doing so may produce thousands of mass spectra in a single experiment which has created a high demand for specialized computational support to analyze these spectral libraries. The computational biology and bioinformatics community has so far established methodology in genomics, transcriptomics and proteomics but there are many (combinatorial) challenges when it comes to structural diversity of lipids and their identification, quantification and interpretation. This review gives an overview and outlook on lipidomics research and illustrates ongoing computational and bioinformatics efforts. These efforts are important and necessary steps to advance the lipidomics field alongside analytic, biochemistry, biomedical and biology communities and to close the gap in available computational methodology between lipidomics and other omics sub-branches.

  6. Lipidomics of glycosphingolipids.

    Science.gov (United States)

    Farwanah, Hany; Kolter, Thomas

    2012-02-02

    Glycosphingolipids (GSLs) contain one or more sugars that are attached to a sphingolipid moiety, usually to a ceramide, but in rare cases also to a sphingoid base. A large structural heterogeneity results from differences in number, identity, linkage, and anomeric configuration of the carbohydrate residues, and also from structural differences within the hydrophobic part. GSLs form complex cell-type specific patterns, which change with the species, the cellular differentiation state, viral transformation, ontogenesis, and oncogenesis. Although GSL structures can be assigned to only a few series with a common carbohydrate core, their structural variety and the complex pattern are challenges for their elucidation and quantification by mass spectrometric techniques. We present a general overview of the application of lipidomics for GSL determination. This includes analytical procedures and instrumentation together with recent correlations of GSL molecular species with human diseases. Difficulties such as the structural complexity and the lack of standard substances for complex GSLs are discussed.

  7. Lipidomics of Glycosphingolipids

    Directory of Open Access Journals (Sweden)

    Hany Farwanah

    2012-02-01

    Full Text Available Glycosphingolipids (GSLs contain one or more sugars that are attached to a sphingolipid moiety, usually to a ceramide, but in rare cases also to a sphingoid base. A large structural heterogeneity results from differences in number, identity, linkage, and anomeric configuration of the carbohydrate residues, and also from structural differences within the hydrophobic part. GSLs form complex cell-type specific patterns, which change with the species, the cellular differentiation state, viral transformation, ontogenesis, and oncogenesis. Although GSL structures can be assigned to only a few series with a common carbohydrate core, their structural variety and the complex pattern are challenges for their elucidation and quantification by mass spectrometric techniques. We present a general overview of the application of lipidomics for GSL determination. This includes analytical procedures and instrumentation together with recent correlations of GSL molecular species with human diseases. Difficulties such as the structural complexity and the lack of standard substances for complex GSLs are discussed.

  8. Reporting of lipidomics data should be standardized

    DEFF Research Database (Denmark)

    Liebisch, Gerhard; Ekroos, Kim; Hermansson, Martin

    2017-01-01

    This article highlights, to our opinion, some of the most pertinent issues related to producing high quality lipidomics data. These issues include pitfalls related to sample collection and storage, lipid extraction, the use of shotgun and LC-MS-based lipidomics approaches, and the identification......, annotation and quantification of lipid species. We hope that highlighting these issues will help stimulate efforts to implement reporting standards for dissemination of lipidomics data. This article is part of a Special Issue entitled: BBALIP_Lipidomics Opinion Articles edited by Sepp Kohlwein....

  9. Lipidomics in vascular health: current perspectives.

    Science.gov (United States)

    Kolovou, Genovefa; Kolovou, Vana; Mavrogeni, Sophie

    2015-01-01

    Identifying the mechanisms that convert a healthy vascular wall to an atherosclerotic wall is of major importance since the consequences may lead to a shortened lifespan. Classical risk factors (age, smoking, obesity, diabetes mellitus, hypertension, and dyslipidemia) may result in the progression of atherosclerotic lesions by processes including inflammation and lipid accumulation. Thus, the evaluation of blood lipids and the full lipid complement produced by cells, organisms, or tissues (lipidomics) is an issue of importance. In this review, we shall describe the recent progress in vascular health research using lipidomic advances. We will begin with an overview of vascular wall biology and lipids, followed by a short analysis of lipidomics. Finally, we shall focus on the clinical implications of lipidomics and studies that have examined lipidomic approaches and vascular health.

  10. MULTI-DIMENSIONAL MASS SPECTROMETRY-BASED SHOTGUN LIPIDOMICS AND NOVEL STRATEGIES FOR LIPIDOMIC ANALYSES

    Science.gov (United States)

    Han, Xianlin; Yang, Kui; Gross, Richard W.

    2011-01-01

    Since our last comprehensive review on multi-dimensional mass spectrometry-based shotgun lipidomics (Mass Spectrom. Rev. 24 (2005), 367), many new developments in the field of lipidomics have occurred. These developments include new strategies and refinements for shotgun lipidomic approaches that use direct infusion, including novel fragmentation strategies, identification of multiple new informative dimensions for mass spectrometric interrogation, and the development of new bioinformatic approaches for enhanced identification and quantitation of the individual molecular constituents that comprise each cell’s lipidome. Concurrently, advances in liquid chromatography-based platforms and novel strategies for quantitative matrix-assisted laser desorption/ionization mass spectrometry for lipidomic analyses have been developed. Through the synergistic use of this repertoire of new mass spectrometric approaches, the power and scope of lipidomics has been greatly expanded to accelerate progress toward the comprehensive understanding of the pleiotropic roles of lipids in biological systems. PMID:21755525

  11. Membrane lipidome of an epithelial cell line

    DEFF Research Database (Denmark)

    Sampaio, Julio L; Gerl, Mathias J; Klose, Christian

    2011-01-01

    Tissue differentiation is an important process that involves major cellular membrane remodeling. We used Madin-Darby canine kidney cells as a model for epithelium formation and investigated the remodeling of the total cell membrane lipidome during the transition from a nonpolarized morphology...... to an epithelial morphology and vice versa. To achieve this, we developed a shotgun-based lipidomics workflow that enabled the absolute quantification of mammalian membrane lipidomes with minimal sample processing from low sample amounts. Epithelial morphogenesis was accompanied by a major shift from sphingomyelin...... to generate an apical membrane domain that serves as a protective barrier for the epithelial sheet....

  12. High-content screening of yeast mutant libraries by shotgun lipidomics

    DEFF Research Database (Denmark)

    Tarasov, Kirill; Stefanko, Adam; Casanovas, Albert

    2014-01-01

    To identify proteins with a functional role in lipid metabolism and homeostasis we designed a high-throughput platform for high-content lipidomic screening of yeast mutant libraries. To this end, we combined culturing and lipid extraction in 96-well format, automated direct infusion...... factor KAR4 precipitated distinct lipid metabolic phenotypes. These results demonstrate that the high-throughput shotgun lipidomics platform is a valid and complementary proxy for high-content screening of yeast mutant libraries....... nanoelectrospray ionization, high-resolution Orbitrap mass spectrometry, and a dedicated data processing framework to support lipid phenotyping across hundreds of Saccharomyces cerevisiae mutants. Our novel approach revealed that the absence of genes with unknown function YBR141C and YJR015W, and the transcription...

  13. Lipidomics profiling reveals the role of glycerophospholipid metabolism in psoriasis.

    Science.gov (United States)

    Zeng, Chunwei; Wen, Bo; Hou, Guixue; Lei, Li; Mei, Zhanlong; Jia, Xuekun; Chen, Xiaomin; Zhu, Wu; Li, Jie; Kuang, Yehong; Zeng, Weiqi; Su, Juan; Liu, Siqi; Peng, Cong; Chen, Xiang

    2017-10-01

    Psoriasis is a common and chronic inflammatory skin disease that is complicated by gene-environment interactions. Although genomic, transcriptomic, and proteomic analyses have been performed to investigate the pathogenesis of psoriasis, the role of metabolites in psoriasis, particularly of lipids, remains unclear. Lipids not only comprise the bulk of the cellular membrane bilayers but also regulate a variety of biological processes such as cell proliferation, apoptosis, immunity, angiogenesis, and inflammation. In this study, an untargeted lipidomics approach was used to study the lipid profiles in psoriasis and to identify lipid metabolite signatures for psoriasis through ultra-performance liquid chromatography-tandem quadrupole mass spectrometry. Plasma samples from 90 participants (45 healthy and 45 psoriasis patients) were collected and analyzed. Statistical analysis was applied to find different metabolites between the disease and healthy groups. In addition, enzyme-linked immunosorbent assay was performed to validate differentially expressed lipids in psoriatic patient plasma. Finally, we identified differential expression of several lipids including lysophosphatidic acid (LPA), lysophosphatidylcholine (LysoPC), phosphatidylinositol (PI), phosphatidylcholine (PC), and phosphatidic acid (PA); among these metabolites, LPA, LysoPC, and PA were significantly increased, while PC and PI were down-regulated in psoriasis patients. We found that elements of glycerophospholipid metabolism such as LPA, LysoPC, PA, PI, and PC were significantly altered in the plasma of psoriatic patients; this study characterizes the circulating lipids in psoriatic patients and provides novel insight into the role of lipids in psoriasis. © The Author 2017. Published by Oxford University Press.

  14. Novel advances in shotgun lipidomics for biology and medicine.

    Science.gov (United States)

    Wang, Miao; Wang, Chunyan; Han, Rowland H; Han, Xianlin

    2016-01-01

    The field of lipidomics, as coined in 2003, has made profound advances and been rapidly expanded. The mass spectrometry-based strategies of this analytical methodology-oriented research discipline for lipid analysis are largely fallen into three categories: direct infusion-based shotgun lipidomics, liquid chromatography-mass spectrometry-based platforms, and matrix-assisted laser desorption/ionization mass spectrometry-based approaches (particularly in imagining lipid distribution in tissues or cells). This review focuses on shotgun lipidomics. After briefly introducing its fundamentals, the major materials of this article cover its recent advances. These include the novel methods of lipid extraction, novel shotgun lipidomics strategies for identification and quantification of previously hardly accessible lipid classes and molecular species including isomers, and novel tools for processing and interpretation of lipidomics data. Representative applications of advanced shotgun lipidomics for biological and biomedical research are also presented in this review. We believe that with these novel advances in shotgun lipidomics, this approach for lipid analysis should become more comprehensive and high throughput, thereby greatly accelerating the lipidomics field to substantiate the aberrant lipid metabolism, signaling, trafficking, and homeostasis under pathological conditions and their underpinning biochemical mechanisms. Copyright © 2015 Elsevier B.V. All rights reserved.

  15. Analytical strategies in lipidomics and applications in disease biomarker discovery

    NARCIS (Netherlands)

    Hu, C.; Heijden, R. van der; Wang, M.; Greef, J. van der; Hankemeier, T.; Xu, G.

    2009-01-01

    Lipidomics is a lipid-targeted metabolomics approach aiming at comprehensive analysis of lipids in biological systems. Recently, lipid profiling, or so-called lipidomics research, has captured increased attention due to the well-recognized roles of lipids in numerous human diseases to which

  16. Lipidomic data analysis: Tutorial, practical guidelines and applications

    Energy Technology Data Exchange (ETDEWEB)

    Checa, Antonio [Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Scheeles väg 2, SE-171 77 Stockholm (Sweden); Bedia, Carmen [Department of Environmental Chemistry, IDAEA-CSIC, Jordi Girona 18–26, Barcelona 08034 (Spain); Jaumot, Joaquim, E-mail: joaquim.jaumot@idaea.csic.es [Department of Environmental Chemistry, IDAEA-CSIC, Jordi Girona 18–26, Barcelona 08034 (Spain)

    2015-07-23

    Highlights: • An overview of chemometric methods applied to lipidomic data analysis is presented. • A lipidomic data set is analyzed showing the strengths of the introduced methods. • Practical guidelines for lipidomic data analysis are discussed. • Examples of applications of lipidomic data analysis in different fields are provided. - Abstract: Lipids are a broad group of biomolecules involved in diverse critical biological roles such as cellular membrane structure, energy storage or cell signaling and homeostasis. Lipidomics is the -omics science that pursues the comprehensive characterization of lipids present in a biological sample. Different analytical strategies such as nuclear magnetic resonance or mass spectrometry with or without previous chromatographic separation are currently used to analyze the lipid composition of a sample. However, current analytical techniques provide a vast amount of data which complicates the interpretation of results without the use of advanced data analysis tools. The choice of the appropriate chemometric method is essential to extract valuable information from the crude data as well as to interpret the lipidomic results in the biological context studied. The present work summarizes the diverse methods of analysis than can be used to study lipidomic data, from statistical inference tests to more sophisticated multivariate analysis methods. In addition to the theoretical description of the methods, application of various methods to a particular lipidomic data set as well as literature examples are presented.

  17. Global analysis of the yeast lipidome by quantitative shotgun mass spectrometry

    DEFF Research Database (Denmark)

    Ejsing, Christer S.; Sampaio, Julio L; Surendranath, Vineeth

    2009-01-01

    95% coverage of the yeast lipidome achieved with 125-fold improvement in sensitivity compared with previous approaches. Comparative lipidomics demonstrated that growth temperature and defects in lipid biosynthesis induce ripple effects throughout the molecular composition of the yeast lipidome....... This work serves as a resource for molecular characterization of eukaryotic lipidomes, and establishes shotgun lipidomics as a powerful platform for complementing biochemical studies and other systems-level approaches....

  18. A lipidomic concept in infectious diseases

    Directory of Open Access Journals (Sweden)

    Khaled Mohamed Mohamed Koriem

    2017-03-01

    Full Text Available Infectious diseases resemble a great threat to the human health according to World Health Organization where about 17% of all deaths (≈9.2 million deaths in 2013 recorded are related to infectious diseases. The pathogenic microorganisms such as bacteria, viruses, fungi and parasites are the principle causes of infectious diseases. Ebola, AIDS, dengue, hepatitis, malaria, tuberculosis and schistosomiasis are among 216 infectious diseases found where the immunity represents the first line defense in infection. Lipidomic includes examination of different biological lipids in the biological cell. The lipidomic research covers all aspects of individual lipid molecule including its structure, function, connection with other cell constituents such as protein, lipid, and metabolite in both health and disease conditions. Details of cell biology obtained from different pathogens (viruses, bacteria, and parasites provide a great data on molecular structure of host-pathogen relation and consequently on infection process. The lipids here play a very important role in many processes involved in host-pathogen relations. The role of lipid in host-pathogen link includes many processes in (1 structural host constituents, (2 host recognition, (3 intracellular transferring, and (4 energy and resource homeostasis during pathogen duplication. There are many lipid phosphatases, kinases, and lipases molecules that greatly involved in these processes and controlling pathogen expression and infection progress. The cell lipid metabolism depends on an adequate energy stores that push the infection to be accelerated and disease symptoms to be appeared. Consequently, future lipidomics studies are the basic for detecting the lipid role in host-pathogen relations which help in therapy advances and biomarkers development.

  19. RNA-Seq and Mass-Spectrometry-Based Lipidomics Reveal Extensive Changes of Glycerolipid Pathways in Brown Adipose Tissue in Response to Cold

    DEFF Research Database (Denmark)

    Marcher, Ann-Britt; Loft, Anne; Nielsen, Ronni

    2015-01-01

    involved in glycerophospholipid synthesis and fatty acid elongation. This is accompanied by significant changes in the acyl chain composition of triacylglycerols (TAGs) as well as subspecies-selective changes of acyl chains in glycerophospholipids. These results indicate that cold adaptation of BAT......Cold exposure greatly alters brown adipose tissue (BAT) gene expression and metabolism to increase thermogenic capacity. Here, we used RNA sequencing and mass-spectrometry-based lipidomics to provide a comprehensive resource describing the molecular signature of cold adaptation at the level...... of the transcriptome and lipidome. We show that short-term (3-day) cold exposure leads to a robust increase in expression of several brown adipocyte genes related to thermogenesis as well as the gene encoding the hormone irisin. However, pathway analysis shows that the most significantly induced genes are those...

  20. MPLEx: a Robust and Universal Protocol for Single-Sample Integrative Proteomic, Metabolomic, and Lipidomic Analyses

    Energy Technology Data Exchange (ETDEWEB)

    Nakayasu, Ernesto S.; Nicora, Carrie D.; Sims, Amy C.; Burnum-Johnson, Kristin E.; Kim, Young-Mo; Kyle, Jennifer E.; Matzke, Melissa M.; Shukla, Anil K.; Chu, Rosalie K.; Schepmoes, Athena A.; Jacobs, Jon M.; Baric, Ralph S.; Webb-Robertson, Bobbie-Jo; Smith, Richard D.; Metz, Thomas O.; Chia, Nicholas

    2016-05-03

    ABSTRACT

    Integrative multi-omics analyses can empower more effective investigation and complete understanding of complex biological systems. Despite recent advances in a range of omics analyses, multi-omic measurements of the same sample are still challenging and current methods have not been well evaluated in terms of reproducibility and broad applicability. Here we adapted a solvent-based method, widely applied for extracting lipids and metabolites, to add proteomics to mass spectrometry-based multi-omics measurements. Themetabolite,protein, andlipidextraction (MPLEx) protocol proved to be robust and applicable to a diverse set of sample types, including cell cultures, microbial communities, and tissues. To illustrate the utility of this protocol, an integrative multi-omics analysis was performed using a lung epithelial cell line infected with Middle East respiratory syndrome coronavirus, which showed the impact of this virus on the host glycolytic pathway and also suggested a role for lipids during infection. The MPLEx method is a simple, fast, and robust protocol that can be applied for integrative multi-omic measurements from diverse sample types (e.g., environmental,in vitro, and clinical).

    IMPORTANCEIn systems biology studies, the integration of multiple omics measurements (i.e., genomics, transcriptomics, proteomics, metabolomics, and lipidomics) has been shown to provide a more complete and informative view of biological pathways. Thus, the prospect of extracting different types of molecules (e.g., DNAs, RNAs, proteins, and metabolites) and performing multiple omics measurements on single samples is very attractive, but such studies are challenging due to the fact that the extraction conditions differ according to the molecule type. Here, we adapted an organic solvent-based extraction method that demonstrated

  1. Lipidomics in research on yeast membrane lipid homeostasis.

    Science.gov (United States)

    de Kroon, Anton I P M

    2017-08-01

    Mass spectrometry is increasingly used in research on membrane lipid homeostasis, both in analyses of the steady state lipidome at the level of molecular lipid species, and in pulse-chase approaches employing stable isotope-labeled lipid precursors addressing the dynamics of lipid metabolism. Here my experience with, and view on mass spectrometry-based lipid analysis is presented, with emphasis on aspects of quantification of membrane lipid composition of the yeast Saccharomyces cerevisiae. This article is part of a Special Issue entitled: BBALIP_Lipidomics Opinion Articles edited by Sepp Kohlwein. Copyright © 2017 Elsevier B.V. All rights reserved.

  2. Shotgun lipidomic analysis of chemically sulfated sterols compromises analytical sensitivity

    DEFF Research Database (Denmark)

    Casanovas, Albert; Hannibal-Bach, Hans Kristian; Jensen, Ole Nørregaard

    2014-01-01

    Shotgun lipidomics affords comprehensive and quantitative analysis of lipid species in cells and tissues at high-throughput [1 5]. The methodology is based on direct infusion of lipid extracts by electrospray ionization (ESI) combined with tandem mass spectrometry (MS/MS) and/or high resolution F...... low ionization efficiency in ESI [7]. For this reason, chemical derivatization procedures including acetylation [8] or sulfation [9] are commonly implemented to facilitate ionization, detection and quantification of sterols for global lipidome analysis [1-3, 10]....

  3. Mass Spectrometry Based Lipidomics: An Overview of Technological Platforms

    Science.gov (United States)

    Köfeler, Harald C.; Fauland, Alexander; Rechberger, Gerald N.; Trötzmüller, Martin

    2012-01-01

    One decade after the genomic and the proteomic life science revolution, new ‘omics’ fields are emerging. The metabolome encompasses the entity of small molecules—Most often end products of a catalytic process regulated by genes and proteins—with the lipidome being its fat soluble subdivision. Within recent years, lipids are more and more regarded not only as energy storage compounds but also as interactive players in various cellular regulation cycles and thus attain rising interest in the bio-medical community. The field of lipidomics is, on one hand, fuelled by analytical technology advances, particularly mass spectrometry and chromatography, but on the other hand new biological questions also drive analytical technology developments. Compared to fairly standardized genomic or proteomic high-throughput protocols, the high degree of molecular heterogeneity adds a special analytical challenge to lipidomic analysis. In this review, we will take a closer look at various mass spectrometric platforms for lipidomic analysis. We will focus on the advantages and limitations of various experimental setups like ‘shotgun lipidomics’, liquid chromatography—Mass spectrometry (LC-MS) and matrix assisted laser desorption ionization-time of flight (MALDI-TOF) based approaches. We will also examine available software packages for data analysis, which nowadays is in fact the rate limiting step for most ‘omics’ workflows. PMID:24957366

  4. Lipidomics of human brain aging and Alzheimer's disease pathology.

    Science.gov (United States)

    Naudí, Alba; Cabré, Rosanna; Jové, Mariona; Ayala, Victoria; Gonzalo, Hugo; Portero-Otín, Manuel; Ferrer, Isidre; Pamplona, Reinald

    2015-01-01

    Lipids stimulated and favored the evolution of the brain. Adult human brain contains a large amount of lipids, and the largest diversity of lipid classes and lipid molecular species. Lipidomics is defined as "the full characterization of lipid molecular species and of their biological roles with respect to expression of proteins involved in lipid metabolism and function, including gene regulation." Therefore, the study of brain lipidomics can help to unravel the diversity and to disclose the specificity of these lipid traits and its alterations in neural (neurons and glial) cells, groups of neural cells, brain, and fluids such as cerebrospinal fluid and plasma, thus helping to uncover potential biomarkers of human brain aging and Alzheimer disease. This review will discuss the lipid composition of the adult human brain. We first consider a brief approach to lipid definition, classification, and tools for analysis from the new point of view that has emerged with lipidomics, and then turn to the lipid profiles in human brain and how lipids affect brain function. Finally, we focus on the current status of lipidomics findings in human brain aging and Alzheimer's disease pathology. Neurolipidomics will increase knowledge about physiological and pathological functions of brain cells and will place the concept of selective neuronal vulnerability in a lipid context. © 2015 Elsevier Inc. All rights reserved.

  5. Mass Spectrometry Based Lipidomics: An Overview of Technological Platforms

    Directory of Open Access Journals (Sweden)

    Harald C. Köfeler

    2012-01-01

    Full Text Available One decade after the genomic and the proteomic life science revolution, new ‘omics’ fields are emerging. The metabolome encompasses the entity of small molecules—Most often end products of a catalytic process regulated by genes and proteins—with the lipidome being its fat soluble subdivision. Within recent years, lipids are more and more regarded not only as energy storage compounds but also as interactive players in various cellular regulation cycles and thus attain rising interest in the bio-medical community. The field of lipidomics is, on one hand, fuelled by analytical technology advances, particularly mass spectrometry and chromatography, but on the other hand new biological questions also drive analytical technology developments. Compared to fairly standardized genomic or proteomic high-throughput protocols, the high degree of molecular heterogeneity adds a special analytical challenge to lipidomic analysis. In this review, we will take a closer look at various mass spectrometric platforms for lipidomic analysis. We will focus on the advantages and limitations of various experimental setups like ‘shotgun lipidomics’, liquid chromatography—Mass spectrometry (LC-MS and matrix assisted laser desorption ionization-time of flight (MALDI-TOF based approaches. We will also examine available software packages for data analysis, which nowadays is in fact the rate limiting step for most ‘omics’ workflows.

  6. Lipidomic analysis of psychrophilic yeasts cultivated at different temperatures

    Czech Academy of Sciences Publication Activity Database

    Řezanka, Tomáš; Kolouchová, I.; Sigler, Karel

    2016-01-01

    Roč. 1861, č. 11 (2016), s. 1634-1642 ISSN 1388-1981 R&D Projects: GA ČR GA14-00227S Institutional support: RVO:61388971 Keywords : Lipidomic analysis * Phosphatidylcholine * Phosphatidylethanolamine Subject RIV: EE - Microbiology, Virology Impact factor: 5.547, year: 2016

  7. Lipidomics: Novel insight into the biochemical mechanism of lipid metabolism and dysregulation-associated disease.

    Science.gov (United States)

    Zhao, Ying-Yong; Miao, Hua; Cheng, Xian-Long; Wei, Feng

    2015-10-05

    The application of lipidomics, after genomics, proteomics and metabolomics, offered largely opportunities to illuminate the entire spectrum of lipidome based on a quantitative or semi-quantitative level in a biological system. When combined with advances in proteomics and metabolomics high-throughput platforms, lipidomics provided the opportunity for analyzing the unique roles of specific lipids in complex cellular processes. Abnormal lipid metabolism was demonstrated to be greatly implicated in many human lifestyle-related diseases. In this review, we focused on lipidomic applications in brain injury disease, cancer, metabolic disease, cardiovascular disease, respiratory disease and infectious disease to discover disease biomarkers and illustrate biochemical metabolic pathways. We also discussed the analytical techniques, future perspectives and potential problems of lipidomic applications. The application of lipidomics in disease biomarker discovery provides the opportunity for gaining novel insights into biochemical mechanism. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

  8. Effects of diet and development on the Drosophila lipidome

    Science.gov (United States)

    Carvalho, Maria; Sampaio, Julio L; Palm, Wilhelm; Brankatschk, Marko; Eaton, Suzanne; Shevchenko, Andrej

    2012-01-01

    Cells produce tens of thousands of different lipid species, but the importance of this complexity in vivo is unclear. Analysis of individual tissues and cell types has revealed differences in abundance of individual lipid species, but there has been no comprehensive study comparing tissue lipidomes within a single developing organism. Here, we used quantitative shotgun profiling by high-resolution mass spectrometry to determine the absolute (molar) content of 250 species of 14 major lipid classes in 6 tissues of animals at 27 developmental stages raised on 4 different diets. Comparing these lipidomes revealed unexpected insights into lipid metabolism. Surprisingly, the fatty acids present in dietary lipids directly influence tissue phospholipid composition throughout the animal. Furthermore, Drosophila differentially regulates uptake, mobilization and tissue accumulation of specific sterols, and undergoes unsuspected shifts in fat metabolism during larval and pupal development. Finally, we observed striking differences between tissue lipidomes that are conserved between phyla. This study provides a comprehensive, quantitative and expandable resource for further pharmacological and genetic studies of metabolic disorders and molecular mechanisms underlying dietary response. PMID:22864382

  9. Age-Associated Lipidome Changes in Metaphase II Mouse Oocytes.

    Directory of Open Access Journals (Sweden)

    Hyuck Jun Mok

    Full Text Available The quality of mammalian oocytes declines with age, which negatively affects fertilization and developmental potential. The aging process often accompanies damages to macromolecules such as proteins, DNA, and lipids. To investigate if aged oocytes display an altered lipidome compared to young oocytes, we performed a global lipidomic analysis between oocytes from 4-week-old and 42 to 50-week-old mice. Increased oxidative stress is often considered as one of the main causes of cellular aging. Thus, we set up a group of 4-week-old oocytes treated with hydrogen peroxide (H2O2, a commonly used oxidative stressor, to compare if similar lipid species are altered between aged and oxidative-stressed oocytes. Between young and aged oocytes, we identified 26 decreased and 6 increased lipids in aged oocytes; and between young and H2O2-treated oocytes, we identified 35 decreased and 26 increased lipids in H2O2-treated oocytes. The decreased lipid species in these two comparisons were overlapped, whereas the increased lipid species were distinct. Multiple phospholipid classes, phosphatidic acid (PA, phosphatidylinositol (PI, phosphatidylserine (PS, and lysophosphatidylserine (LPS significantly decreased both in H2O2-treated and aged oocytes, suggesting that the integrity of plasma membrane is similarly affected under these conditions. In contrast, a dramatic increase in diacylglycerol (DG was only noted in H2O2-treated oocytes, indicating that the acute effect of H2O2-caused oxidative stress is distinct from aging-associated lipidome alteration. In H2O2-treated oocytes, the expression of lysophosphatidylcholine acyltransferase 1 increased along with increases in phosphatidylcholine. Overall, our data reveal that several classes of phospholipids are affected in aged oocytes, suggesting that the integrity of plasma membrane is associated with maintaining fertilization and developmental potential of mouse oocytes.

  10. Blood plasma lipidomic signature of epicardial fat in healthy obese women.

    Science.gov (United States)

    Scherer, Max; Montoliu, Ivan; Qanadli, Salah D; Collino, Sebastiano; Rezzi, Serge; Kussmann, Martin; Giusti, Vittorio; Martin, François-Pierre J

    2015-01-01

    A lipidomic approach was employed in a clinically well-defined cohort of healthy obese women to explore blood lipidome phenotype ascribed to body fat deposition, with emphasis on epicardial adipose tissue (EAT). The present investigation delivered a lipidomics signature of epicardial adiposity under healthy clinical conditions using a cohort of 40 obese females (age: 25-45 years, BMI: 28-40 kg/m(2) ) not showing any metabolic disease traits. Lipidomics analysis of blood plasma was employed in combination with in vivo quantitation of mediastinal fat depots by computerized tomography. All cardiac fat depots correlated to indicators of hepatic dysfunctions (ALAT and ASAT), which describe physiological connections between hepatic and cardiac steatosis. Plasma lipidomics encompassed overall levels of lipid classes, fatty acid profiles, and individual lipid species. EAT and visceral fat associated with diacylglycerols (DAG), triglycerides, and distinct phospholipid and sphingolipid species. A pattern of DAG and phosphoglycerols was specific to EAT. Human blood plasma lipidomics appears to be a promising clinical and potentially diagnostic readout for patient stratification and monitoring. Association of blood lipidomics signature to regio-specific mediastinal and visceral adiposity under healthy clinical conditions may help provide more biological insights into obese patient stratification for cardiovascular disease risks. © 2014 The Obesity Society.

  11. Lipidomic Analysis of Chlamydomonas reinhardtii under Nitrogen and Sulfur Deprivation.

    Directory of Open Access Journals (Sweden)

    Dawei Yang

    Full Text Available Chlamydomonas reinhardtii accumulates lipids under complete nutrient starvation conditions while overall growth in biomass stops. In order to better understand biochemical changes under nutrient deprivation that maintain production of algal biomass, we used a lipidomic assay for analyzing the temporal regulation of the composition of complex lipids in C. reinhardtii in response to nitrogen and sulfur deprivation. Using a chip-based nanoelectrospray direct infusion into an ion trap mass spectrometer, we measured a diversity of lipid species reported for C. reinhardtii, including PG phosphatidylglycerols, PI Phosphatidylinositols, MGDG monogalactosyldiacylglycerols, DGDG digalactosyldiacylglycerols, SQDG sulfoquinovosyldiacylglycerols, DGTS homoserine ether lipids and TAG triacylglycerols. Individual lipid species were annotated by matching mass precursors and MS/MS fragmentations to the in-house LipidBlast mass spectral database and MS2Analyzer. Multivariate statistics showed a clear impact on overall lipidomic phenotypes on both the temporal and the nutrition stress level. Homoserine-lipids were found up-regulated at late growth time points and higher cell density, while triacyclglycerols showed opposite regulation of unsaturated and saturated fatty acyl chains under nutritional deprivation.

  12. Lipidomic Evaluation of Feline Neurologic Disease after AAV Gene Therapy

    Directory of Open Access Journals (Sweden)

    Heather L. Gray-Edwards

    2017-09-01

    Full Text Available GM1 gangliosidosis is a fatal lysosomal disorder, for which there is no effective treatment. Adeno-associated virus (AAV gene therapy in GM1 cats has resulted in a greater than 6-fold increase in lifespan, with many cats remaining alive at >5.7 years of age, with minimal clinical signs. Glycolipids are the principal storage product in GM1 gangliosidosis whose pathogenic mechanism is not completely understood. Targeted lipidomics analysis was performed to better define disease mechanisms and identify markers of disease progression for upcoming clinical trials in humans. 36 sphingolipids and subspecies associated with ganglioside biosynthesis were tested in the cerebrospinal fluid of untreated GM1 cats at a humane endpoint (∼8 months, AAV-treated GM1 cats (∼5 years old, and normal adult controls. In untreated GM1 cats, significant alterations were noted in 16 sphingolipid species, including gangliosides (GM1 and GM3, lactosylceramides, ceramides, sphingomyelins, monohexosylceramides, and sulfatides. Variable degrees of correction in many lipid metabolites reflected the efficacy of AAV gene therapy. Sphingolipid levels were highly predictive of neurologic disease progression, with 11 metabolites having a coefficient of determination (R2 > 0.75. Also, a specific detergent additive significantly increased the recovery of certain lipid species in cerebrospinal fluid samples. This report demonstrates the methodology and utility of targeted lipidomics to examine the pathophysiology of lipid storage disorders.

  13. Sphingolipids in human synovial fluid--a lipidomic study.

    Directory of Open Access Journals (Sweden)

    Marta Krystyna Kosinska

    Full Text Available Articular synovial fluid (SF is a complex mixture of components that regulate nutrition, communication, shock absorption, and lubrication. Alterations in its composition can be pathogenic. This lipidomic investigation aims to quantify the composition of sphingolipids (sphingomyelins, ceramides, and hexosyl- and dihexosylceramides and minor glycerophospholipid species, including (lysophosphatidic acid, (lysophosphatidylglycerol, and bis(monoacylglycerophosphate species, in the SF of knee joints from unaffected controls and from patients with early (eOA and late (lOA stages of osteoarthritis (OA, and rheumatoid arthritis (RA. SF without cells and cellular debris from 9 postmortem donors (control, 18 RA, 17 eOA, and 13 lOA patients were extracted to measure lipid species using electrospray ionization tandem mass spectrometry--directly or coupled with hydrophilic interaction liquid chromatography. We provide a novel, detailed overview of sphingolipid and minor glycerophospholipid species in human SF. A total of 41, 48, and 50 lipid species were significantly increased in eOA, lOA, and RA SF, respectively when compared with normal SF. The level of 21 lipid species differed in eOA SF versus SF from lOA, an observation that can be used to develop biomarkers. Sphingolipids can alter synovial inflammation and the repair responses of damaged joints. Thus, our lipidomic study provides the foundation for studying the biosynthesis and function of lipid species in health and most prevalent joint diseases.

  14. Lipidomics reveals a remarkable diversity of lipids in human plasma.

    Science.gov (United States)

    Quehenberger, Oswald; Armando, Aaron M; Brown, Alex H; Milne, Stephen B; Myers, David S; Merrill, Alfred H; Bandyopadhyay, Sibali; Jones, Kristin N; Kelly, Samuel; Shaner, Rebecca L; Sullards, Cameron M; Wang, Elaine; Murphy, Robert C; Barkley, Robert M; Leiker, Thomas J; Raetz, Christian R H; Guan, Ziqiang; Laird, Gregory M; Six, David A; Russell, David W; McDonald, Jeffrey G; Subramaniam, Shankar; Fahy, Eoin; Dennis, Edward A

    2010-11-01

    The focus of the present study was to define the human plasma lipidome and to establish novel analytical methodologies to quantify the large spectrum of plasma lipids. Partial lipid analysis is now a regular part of every patient's blood test and physicians readily and regularly prescribe drugs that alter the levels of major plasma lipids such as cholesterol and triglycerides. Plasma contains many thousands of distinct lipid molecular species that fall into six main categories including fatty acyls, glycerolipids, glycerophospholipids, sphingolipids, sterols, and prenols. The physiological contributions of these diverse lipids and how their levels change in response to therapy remain largely unknown. As a first step toward answering these questions, we provide herein an in-depth lipidomics analysis of a pooled human plasma obtained from healthy individuals after overnight fasting and with a gender balance and an ethnic distribution that is representative of the US population. In total, we quantitatively assessed the levels of over 500 distinct molecular species distributed among the main lipid categories. As more information is obtained regarding the roles of individual lipids in health and disease, it seems likely that future blood tests will include an ever increasing number of these lipid molecules.

  15. High-throughput shotgun lipidomics by quadrupole time-of-flight mass spectrometry

    DEFF Research Database (Denmark)

    Ståhlman, Marcus; Ejsing, Christer S.; Tarasov, Kirill

    2009-01-01

    Technological advances in mass spectrometry and meticulous method development have produced several shotgun lipidomic approaches capable of characterizing lipid species by direct analysis of total lipid extracts. Shotgun lipidomics by hybrid quadrupole time-of-flight mass spectrometry allows...... the absolute quantification of hundreds of molecular glycerophospholipid species, glycerolipid species, sphingolipid species and sterol lipids. Future applications in clinical cohort studies demand detailed lipid molecule information and the application of high-throughput lipidomics platforms. In this review...... we describe a novel high-throughput shotgun lipidomic platform based on 96-well robot-assisted lipid extraction, automated sample infusion by mircofluidic-based nanoelectrospray ionization, and quantitative multiple precursor ion scanning analysis on a quadrupole time-of-flight mass spectrometer...

  16. Lipidomic analysis of epidermal lipids: a tool to predict progression of inflammatory skin disease in humans.

    Science.gov (United States)

    Li, Shan; Ganguli-Indra, Gitali; Indra, Arup K

    2016-05-01

    Lipidomics is the large-scale profiling and characterization of lipid species in a biological system using mass spectrometry. The skin barrier is mainly comprised of corneocytes and a lipid-enriched extracellular matrix. The major skin lipids are ceramides, cholesterol and free fatty acids (FFA). Lipid compositions are altered in inflammatory skin disorders with disrupted skin barrier such as atopic dermatitis (AD). Here we discuss some of the recent applications of lipidomics in human skin biology and in inflammatory skin diseases such as AD, psoriasis and Netherton syndrome. We also review applications of lipidomics in human skin equivalent and in pre-clinical animal models of skin diseases to gain insight into the pathogenesis of the skin disease. Expert commentary: Skin lipidomics analysis could be a fast, reliable and noninvasive tool to characterize the skin lipid profile and to monitor the progression of inflammatory skin diseases such as AD.

  17. Analysis of lipid experiments (ALEX: a software framework for analysis of high-resolution shotgun lipidomics data.

    Directory of Open Access Journals (Sweden)

    Peter Husen

    Full Text Available Global lipidomics analysis across large sample sizes produces high-content datasets that require dedicated software tools supporting lipid identification and quantification, efficient data management and lipidome visualization. Here we present a novel software-based platform for streamlined data processing, management and visualization of shotgun lipidomics data acquired using high-resolution Orbitrap mass spectrometry. The platform features the ALEX framework designed for automated identification and export of lipid species intensity directly from proprietary mass spectral data files, and an auxiliary workflow using database exploration tools for integration of sample information, computation of lipid abundance and lipidome visualization. A key feature of the platform is the organization of lipidomics data in "database table format" which provides the user with an unsurpassed flexibility for rapid lipidome navigation using selected features within the dataset. To demonstrate the efficacy of the platform, we present a comparative neurolipidomics study of cerebellum, hippocampus and somatosensory barrel cortex (S1BF from wild-type and knockout mice devoid of the putative lipid phosphate phosphatase PRG-1 (plasticity related gene-1. The presented framework is generic, extendable to processing and integration of other lipidomic data structures, can be interfaced with post-processing protocols supporting statistical testing and multivariate analysis, and can serve as an avenue for disseminating lipidomics data within the scientific community. The ALEX software is available at www.msLipidomics.info.

  18. Analysis of lipid experiments (ALEX): a software framework for analysis of high-resolution shotgun lipidomics data.

    Science.gov (United States)

    Husen, Peter; Tarasov, Kirill; Katafiasz, Maciej; Sokol, Elena; Vogt, Johannes; Baumgart, Jan; Nitsch, Robert; Ekroos, Kim; Ejsing, Christer S

    2013-01-01

    Global lipidomics analysis across large sample sizes produces high-content datasets that require dedicated software tools supporting lipid identification and quantification, efficient data management and lipidome visualization. Here we present a novel software-based platform for streamlined data processing, management and visualization of shotgun lipidomics data acquired using high-resolution Orbitrap mass spectrometry. The platform features the ALEX framework designed for automated identification and export of lipid species intensity directly from proprietary mass spectral data files, and an auxiliary workflow using database exploration tools for integration of sample information, computation of lipid abundance and lipidome visualization. A key feature of the platform is the organization of lipidomics data in "database table format" which provides the user with an unsurpassed flexibility for rapid lipidome navigation using selected features within the dataset. To demonstrate the efficacy of the platform, we present a comparative neurolipidomics study of cerebellum, hippocampus and somatosensory barrel cortex (S1BF) from wild-type and knockout mice devoid of the putative lipid phosphate phosphatase PRG-1 (plasticity related gene-1). The presented framework is generic, extendable to processing and integration of other lipidomic data structures, can be interfaced with post-processing protocols supporting statistical testing and multivariate analysis, and can serve as an avenue for disseminating lipidomics data within the scientific community. The ALEX software is available at www.msLipidomics.info.

  19. Serum lipidomics analysis of ovariectomized rats under Curcuma comosa treatment.

    Science.gov (United States)

    Vinayavekhin, Nawaporn; Sueajai, Jetjamnong; Chaihad, Nichaboon; Panrak, Ratchanee; Chokchaisiri, Ratchanaporn; Sangvanich, Polkit; Suksamrarn, Apichart; Piyachaturawat, Pawinee

    2016-11-04

    Curcuma comosa Roxb. (C. comosa) or Wan Chak Motluk, Zingiberaceae family, has been used in Thai traditional medicine for the treatment of gynecological problems and inflammation. This study aimed to investigate the therapeutic potential of C. comosa by determining the changes in the lipid profiles in the ovariectomized rats, as a model of estrogen-deficiency-induced hyperlipidemia, after treatment with different components of C. comosa using an untargeted lipidomics approach. Lipids were extracted from the serum of adult female rats subjected to a sham operation (SHAM; control), ovariectomy (OVX), or OVX with 12-week daily doses of estrogen (17β-estradiol; E 2 ), (3R)-1,7-diphenyl-(4E,6E)-4,6-heptadien-3-ol (DPHD; a phytoestrogen from C. comosa), powdered C. comosa rhizomes or its crude ethanol extract. They were then analyzed by liquid chromatography-mass spectrometry, characterized, and subjected to the orthogonal projections to latent structures discriminant analysis statistical model to identify tentative biomarkers. Levels of five classes of lipids (ceramide, ceramide-1-phosphate, sphingomyelin, 1-O-alkenyl-lysophosphatidylethanolamine and lysophosphatidylethanolamine) were elevated in the OVX rats compared to those in the SHAM rats, while the monoacylglycerols and triacylglycerols were decreased. The E 2 treatment only reversed the levels of ceramides, whereas treatments with DPHD, C. comosa extract or powder returned the levels of all upregulated lipids back to those in the SHAM control rats. The findings suggest the potential beneficial effects of C. comosa on preventing the increased ceramide levels in OVX rats, a possible cause of metabolic disturbance under estrogen deficiency. Overall, the results demonstrated the power of untargeted lipidomics in discovering disease-relevant biomarkers, as well as evaluating the effectiveness of treatment by C. comosa components (DPHD, extract or powder) as utilized in Thai traditional medicine, and also providing

  20. Differential network analysis with multiply imputed lipidomic data.

    Directory of Open Access Journals (Sweden)

    Maiju Kujala

    Full Text Available The importance of lipids for cell function and health has been widely recognized, e.g., a disorder in the lipid composition of cells has been related to atherosclerosis caused cardiovascular disease (CVD. Lipidomics analyses are characterized by large yet not a huge number of mutually correlated variables measured and their associations to outcomes are potentially of a complex nature. Differential network analysis provides a formal statistical method capable of inferential analysis to examine differences in network structures of the lipids under two biological conditions. It also guides us to identify potential relationships requiring further biological investigation. We provide a recipe to conduct permutation test on association scores resulted from partial least square regression with multiple imputed lipidomic data from the LUdwigshafen RIsk and Cardiovascular Health (LURIC study, particularly paying attention to the left-censored missing values typical for a wide range of data sets in life sciences. Left-censored missing values are low-level concentrations that are known to exist somewhere between zero and a lower limit of quantification. To make full use of the LURIC data with the missing values, we utilize state of the art multiple imputation techniques and propose solutions to the challenges that incomplete data sets bring to differential network analysis. The customized network analysis helps us to understand the complexities of the underlying biological processes by identifying lipids and lipid classes that interact with each other, and by recognizing the most important differentially expressed lipids between two subgroups of coronary artery disease (CAD patients, the patients that had a fatal CVD event and the ones who remained stable during two year follow-up.

  1. Complementary and Integrative Medicine

    Science.gov (United States)

    ... medical treatments that are not part of mainstream medicine. When you are using these types of care, it may be called complementary, integrative, or alternative medicine. Complementary medicine is used together with mainstream medical ...

  2. Complementary and Alternative Medicine

    Science.gov (United States)

    ... for Educators Search English Español Complementary and Alternative Medicine KidsHealth / For Teens / Complementary and Alternative Medicine What's ... a replacement. How Is CAM Different From Conventional Medicine? Conventional medicine is based on scientific knowledge of ...

  3. Lipidomic Analysis of Endocannabinoid Signaling: Targeted Metabolite Identification and Quantification

    Directory of Open Access Journals (Sweden)

    Jantana Keereetaweep

    2016-01-01

    Full Text Available The endocannabinoids N-arachidonoylethanolamide (or anandamide, AEA and 2-arachidonoylglycerol (2-AG belong to the larger groups of N-acylethanolamines (NAEs and monoacylglycerol (MAG lipid classes, respectively. They are biologically active lipid molecules that activate G-protein-coupled cannabinoid receptors found in various organisms. After AEA and 2-AG were discovered in the 1990s, they have been extensively documented to have a broad range of physiological functions. Along with AEA, several NAEs, for example, N-palmitoylethanolamine (PEA, N-stearoylethanolamine (SEA, and N-oleoylethanolamine (OEA are also present in tissues, usually at much larger concentrations than AEA. Any perturbation that involves the endocannabinoid pathway may subsequently alter basal level or metabolism of these lipid mediators. Further, the altered levels of these molecules often reflect pathological conditions associated with tissue damage. Robust and sensitive methodologies to analyze these lipid mediators are essential to understanding how they act as endocannabinoids. The recent advances in mass spectrometry allow researchers to develop lipidomics approaches and several methodologies have been proposed to quantify endocannabinoids in various biological systems.

  4. Aberrant Lipid Metabolism in Hepatocellular Carcinoma Revealed by Liver Lipidomics

    Directory of Open Access Journals (Sweden)

    Zhao Li

    2017-11-01

    Full Text Available Background: The aim of this study was to characterize the disorder of lipid metabolism in hepatocellular carcinoma (HCC. HCC is a worldwide disease. The research into the disorder of lipid metabolism in HCC is very limited. Study of lipid metabolism in liver cancer tissue may have the potential to provide new insight into HCC mechanisms. Methods: A lipidomics study of HCC based on Ultra high performance liquid chromatography-electronic spray ionization-QTOF mass spectrometer (UPLC-ESI-QTOF MS and Matrix assisted laser desorption ionization-fourier transform ion cyclotron resonance mass spectrometer (MALDI-FTICR MS was performed. Results: Triacylglycerols (TAGs with the number of double bond (DB > 2 (except 56:5 and 56:4 TAG were significantly down-regulated; conversely, others (except 52:2 TAG were greatly up-regulated in HCC tissues. Moreover, the more serious the disease was, the higher the saturated TAG concentration and the lower the polyunsaturated TAG concentration were in HCC tissues. The phosphatidylcholine (PC, phosphatidylethanolamine (PE and phosphatidylinositol (PI were altered in a certain way. Sphingomyelin (SM was up-regulated and ceramide (Cer were down-regulated in HCC tissues. Conclusions: To our knowledge, this is the first such report showing a unique trend of TAG, PC, PE and PI. The use of polyunsaturated fatty acids, like eicosapentanoic and docosahexanoic acid, as supplementation, proposed for the treatment of Non-alcoholic steatohepatitis (NASH, may also be effective for the treatment of HCC.

  5. Lipidomic analysis of Arabidopsis seed genetically engineered to contain DHA

    Directory of Open Access Journals (Sweden)

    Xue-Rong eZhou

    2014-09-01

    Full Text Available Metabolic engineering of omega-3 long-chain (≥C20 polyunsaturated fatty acids (ω3 LC-PUFA in oilseeds has been one of the key metabolic engineering targets in recent years. By expressing a transgenic pathway for enhancing the synthesis of the ω3 LC-PUFA docosahexaenoic acid (DHA from endogenous -linolenic acid (ALA, we obtained the production of fish oil-like proportions of DHA in Arabidopsis seed oil. Liquid chromatography-mass spectrometry (LC-MS was used to characterize the triacylglycerol (TAG, diacylglycerol (DAG and phospholipid (PL lipid classes in the transgenic and wild type Arabidopsis seeds at both developing and mature stages. The analysis identified the appearance of several abundant DHA-containing phosphatidylcholine (PC, DAG and TAG molecular species in mature seeds. The relative abundances of PL, DAG and TAG species showed a preferred combination of LC-PUFA with ALA in the transgenic seeds, where LC-PUFA were esterified in positions usually occupied by 20:1ω9. Trace amounts of di-DHA PC and tri-DHA TAG were identified, and confirmed by high resolution MS/MS. Studying the lipidome in transgenic seeds provides insights into where DHA accumulated and composed with other fatty acids of neutral and phospholipids from the developing and mature seeds.

  6. Lipidomic mass spectrometry and its application in neuroscience

    Institute of Scientific and Technical Information of China (English)

    Mabel; Enriquez-Algeciras; Sanjoy; K; Bhattacharya

    2013-01-01

    Central and peripheral nervous systems are lipid rich tissues. Lipids, in the context of lipid-protein complexes, surround neurons and provide electrical insulation for transmission of signals allowing neurons to remain embedded within a conducting environment. Lipids play a key role in vesicle formation and fusion in synapses. They provide means of rapid signaling, cell motility and migration for astrocytes and other cell types that surround and play supporting roles neurons. Unlike many other signaling molecules, lipids are capable of multiple signaling events based on the different fragments generated from a single precursor during each event. Lipidomics, until recently suffered from two major disadvantages:(1) level of expertise required an overwhelming amount of chemical detail to correctly identify a vast number of different lipids which could be close in their chemical reactivity; and(2) high amount of purified compounds needed by analytical techniques to determine their structures. Advances in mass spectrometry have enabled overcoming these two limitations. Mass spectrometry offers a great degree of simplicity in identification and quantification of lipids directly extracted from complex biological mixtures. Mass spectrometers can be regarded to as mass analyzers. There are those that separate and analyze the product ion fragments in space(spatial) and those which separate product ions in time in the same space(temporal). Databases and standardized instrument parameters have further aided the capabilities of the spatial instruments while recent advances in bioinformatics have made the identification and quantification possible using temporal instruments.

  7. Lipidomic analysis of immune activation in equine leptospirosis and Leptospira-vaccinated horses.

    Science.gov (United States)

    Wood, Paul L; Steinman, Margaret; Erol, Erdal; Carter, Craig; Christmann, Undine; Verma, Ashutosh

    2018-01-01

    Currently available diagnostic assays for leptospirosis cannot differentiate vaccine from infection serum antibody. Several leptospiral proteins that are upregulated during infection have been described, but their utility as a diagnostic marker is still unclear. In this study, we undertook a lipidomics approach to determine if there are any differences in the serum lipid profiles of horses naturally infected with pathogenic Leptospira spp. and horses vaccinated against a commercially available bacterin. Utilizing a high-resolution mass spectrometry serum lipidomics analytical platform, we demonstrate that cyclic phosphatidic acids, diacylglycerols, and hydroperoxide oxidation products of choline plasmalogens are elevated in the serum of naturally infected as well as vaccinated horses. Other lipids of interest were triacylglycerols that were only elevated in the serum of infected horses and sphingomyelins that were increased only in the serum of vaccinated horses. This is the first report looking at the equine serum lipidome during leptospiral infection and vaccination.

  8. Lipidomic analysis of immune activation in equine leptospirosis and Leptospira-vaccinated horses.

    Directory of Open Access Journals (Sweden)

    Paul L Wood

    Full Text Available Currently available diagnostic assays for leptospirosis cannot differentiate vaccine from infection serum antibody. Several leptospiral proteins that are upregulated during infection have been described, but their utility as a diagnostic marker is still unclear. In this study, we undertook a lipidomics approach to determine if there are any differences in the serum lipid profiles of horses naturally infected with pathogenic Leptospira spp. and horses vaccinated against a commercially available bacterin. Utilizing a high-resolution mass spectrometry serum lipidomics analytical platform, we demonstrate that cyclic phosphatidic acids, diacylglycerols, and hydroperoxide oxidation products of choline plasmalogens are elevated in the serum of naturally infected as well as vaccinated horses. Other lipids of interest were triacylglycerols that were only elevated in the serum of infected horses and sphingomyelins that were increased only in the serum of vaccinated horses. This is the first report looking at the equine serum lipidome during leptospiral infection and vaccination.

  9. Lipidomics in translational research and the clinical significance of lipid-based biomarkers.

    Science.gov (United States)

    Stephenson, Daniel J; Hoeferlin, L Alexis; Chalfant, Charles E

    2017-11-01

    Lipidomics is a rapidly developing field of study that focuses on the identification and quantitation of various lipid species in the lipidome. Lipidomics has now emerged in the forefront of scientific research due to the importance of lipids in metabolism, cancer, and disease. Using both targeted and untargeted mass spectrometry as a tool for analysis, progress in the field has rapidly progressed in the last decade. Having the ability to assess these small molecules in vivo has led to better understanding of several lipid-driven mechanisms and the identification of lipid-based biomarkers in neurodegenerative disease, cancer, sepsis, wound healing, and pre-eclampsia. Biomarker identification and mechanistic understanding of specific lipid pathways linked to a disease's pathologies can form the foundation in the development of novel therapeutics in hopes of curing human disease. Published by Elsevier Inc.

  10. Molecular lipidomics of exosomes released by PC-3 prostate cancer cells

    DEFF Research Database (Denmark)

    Llorente, A.; Skotland, T.; Sylvanne, T.

    2013-01-01

    The molecular lipid composition of exosomes is largely unknown. In this study, sophisticated shotgun and targeted molecular lipidomic assays were performed for in-depth analysis of the lipidomes of the metastatic prostate cancer cell line, PC-3, and their released exosomes. This study, based...... in the quantification of approximately 280 molecular lipid species, provides the most extensive lipid analysis of cells and exosomes to date. Interestingly, major differences were found in the lipid composition of exosomes compared to parent cells. Exosomes show a remarkable enrichment of distinct lipids, demonstrating...... potentially be used as cancer biomarkers. (C) 2013 Elsevier B.V. All rights reserved....

  11. Modulation of the Lactobacillus acidophilus La-5 lipidome by different growth conditions

    DEFF Research Database (Denmark)

    Hansen, Marie-Louise R W; Clausen, Anders; Ejsing, Christer S

    2015-01-01

    Probiotics are bacteria used in the food industry due to their potential health benefits. In this study, the plasma membrane of the probiotic Lactobacillus acidophilus La-5 was investigated using state-of-the-art high-resolution shotgun lipidomics. Comparisons of the lipidome of the plasma membrane...... (CL) and lowest proportion of monolysocardiolipin (MLCL). No significant changes were found for other lipid classes. The bacteria grown with di- and tri-unsaturated fatty acids were expected to have more unsaturated plasma membranes than bacteria grown with mono-unsaturated fatty acids. This was also...

  12. Quantitative analysis of proteome and lipidome dynamics reveals functional regulation of global lipid metabolism

    DEFF Research Database (Denmark)

    Casanovas, Albert; Sprenger, Richard R; Tarasov, Kirill

    2015-01-01

    Elucidating how and to what extent lipid metabolism is remodeled under changing conditions is essential for understanding cellular physiology. Here, we analyzed proteome and lipidome dynamics to investigate how regulation of lipid metabolism at the global scale supports remodeling of cellular...

  13. Changes in the Lipidomic Profile of Aqueous Humor in Open-Angle Glaucoma

    DEFF Research Database (Denmark)

    Cabrerizo, Javier; Urcola, Javier A; Vecino, Elena

    2017-01-01

    PURPOSE: To identify and determine differences in lipid profiles of aqueous humor (AH) in patients with open-angle glaucoma (OAG). MATERIALS AND METHODS: The lipidomic profile of 10 samples of AH of patients with OAG and 10 controls was analyzed. Patients with a history of anterior segment surgery...

  14. Hierarchical clustering analysis of blood plasma lipidomics profiles from mono- and dizygotic twin families

    NARCIS (Netherlands)

    Draisma, H.H.; Reijmers, T.H.; Meulman, J.J.; Greef, J. van der; Hankemeier, T.; Boomsma, D.I.

    2013-01-01

    Twin and family studies are typically used to elucidate the relative contribution of genetic and environmental variation to phenotypic variation. Here, we apply a quantitative genetic method based on hierarchical clustering, to blood plasma lipidomics data obtained in a healthy cohort consisting of

  15. Complementary and Alternative Medicine

    Science.gov (United States)

    ... therapies are often lacking; therefore, the safety and effectiveness of many CAM therapies are uncertain. The National Center for Complementary and Alternative Medicine (NCCAM) is sponsoring research designed to fill this ...

  16. Avocado fruit maturation and ripening: dynamics of aliphatic acetogenins and lipidomic profiles from mesocarp, idioblasts and seed.

    Science.gov (United States)

    Rodríguez-López, Carlos Eduardo; Hernández-Brenes, Carmen; Treviño, Víctor; Díaz de la Garza, Rocío I

    2017-09-29

    Avocado fruit contains aliphatic acetogenins (oft-acetylated, odd-chain fatty alcohols) with promising bioactivities for both medical and food industries. However, we have scarce knowledge about their metabolism. The present work aimed to study changes in acetogenin profiles from mesocarp, lipid-containing idioblasts, and seeds from 'Hass' cultivar during fruit development, germination, and three harvesting years. An untargeted LC-MS based lipidomic analysis was also conducted to profile the lipidome of avocado fruit in each tissue. The targeted analysis showed that acetogenin profiles and contents remained unchanged in avocado mesocarp during maturation and postharvest ripening, germination, and different harvesting years. However, a shift in the acetogenin profile distribution, accompanied with a sharp increase in concentration, was observed in seed during early maturation. Untargeted lipidomics showed that this shift was accompanied with remodeling of glycerolipids: TAGs and DAGs decreased during fruit growing in seed. Remarkably, the majority of the lipidome in mature seed was composed by acetogenins; we suggest that this tissue is able to synthesize them independently from mesocarp. On the other hand, lipid-containing idioblasts accumulated almost the entire acetogenin pool measured in the whole mesocarp, while only having 4% of the total fatty acids. The lipidome of this cell type changed the most when the fruit was ripening after harvesting, TAGs decreased while odd-chain DAGs increased. Notably, idioblast lipidome was more diverse than that from mesocarp. Evidence shown here suggests that idioblasts are the main site of acetogenin biosynthesis in avocado mesocarp. This work unveiled the prevalence of aliphatic acetogenins in the avocado fruit lipidome and evidenced TAGs as initial donors of the acetogenin backbones in its biosynthesis. It also sets evidence for acetogenins being included in future works aimed at characterizing the avocado seed, as they are

  17. Reptilian Transcriptomes v2.0: An Extensive Resource for Sauropsida Genomics and Transcriptomics.

    Science.gov (United States)

    Tzika, Athanasia C; Ullate-Agote, Asier; Grbic, Djordje; Milinkovitch, Michel C

    2015-07-01

    Despite the availability of deep-sequencing techniques, genomic and transcriptomic data remain unevenly distributed across phylogenetic groups. For example, reptiles are poorly represented in sequence databases, hindering functional evolutionary and developmental studies in these lineages substantially more diverse than mammals. In addition, different studies use different assembly and annotation protocols, inhibiting meaningful comparisons. Here, we present the "Reptilian Transcriptomes Database 2.0," which provides extensive annotation of transcriptomes and genomes from species covering the major reptilian lineages. To this end, we sequenced normalized complementary DNA libraries of multiple adult tissues and various embryonic stages of the leopard gecko and the corn snake and gathered published reptilian sequence data sets from representatives of the four extant orders of reptiles: Squamata (snakes and lizards), the tuatara, crocodiles, and turtles. The LANE runner 2.0 software was implemented to annotate all assemblies within a single integrated pipeline. We show that this approach increases the annotation completeness of the assembled transcriptomes/genomes. We then built large concatenated protein alignments of single-copy genes and inferred phylogenetic trees that support the positions of turtles and the tuatara as sister groups of Archosauria and Squamata, respectively. The Reptilian Transcriptomes Database 2.0 resource will be updated to include selected new data sets as they become available, thus making it a reference for differential expression studies, comparative genomics and transcriptomics, linkage mapping, molecular ecology, and phylogenomic analyses involving reptiles. The database is available at www.reptilian-transcriptomes.org and can be enquired using a wwwblast server installed at the University of Geneva. © The Author(s) 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  18. Web services for transcriptomics

    NARCIS (Netherlands)

    Neerincx, P.

    2009-01-01

    Transcriptomics is part of a family of disciplines focussing on high throughput molecular biology experiments. In the case of transcriptomics, scientists study the expression of genes resulting in transcripts. These transcripts can either perform a biological function themselves or function as

  19. Lipidome as a predictive tool in progression to type 2 diabetes in Finnish men

    DEFF Research Database (Denmark)

    Suvitaival, Tommi; Bondia-Pons, Isabel; Yetukuri, Laxman

    2018-01-01

    are not helpful at distinguishing progressors from non-progressors. BACKGROUND: There is a need for early markers to track and predict the development of type 2 diabetes mellitus (T2DM) from the state of normal glucose tolerance through prediabetes. In this study we tested whether the plasma molecular lipidome...... has biomarker potential to predicting the onset of T2DM. METHODS: We applied global lipidomic profiling on plasma samples from well-phenotyped men (107 cases, 216 controls) participating in the longitudinal METSIM study at baseline and at five-year follow-up. To validate the lipid markers......RESULTS: A persistent lipid signature with higher levels of triacylglycerols and diacyl-phospholipids as well as lower levels of alkylacyl phosphatidylcholines was observed in progressors to T2DM. Lysophosphatidylcholine acyl C18:2 (LysoPC(18:2)), phosphatidylcholines PC(32:1), PC(34:2e) and PC(36...

  20. Association of Lipidome Remodeling in the Adipocyte Membrane with Acquired Obesity in Humans

    DEFF Research Database (Denmark)

    Pietilainen, K. H.; Rog, T.; Seppanen-Laakso, T.

    2011-01-01

    Identification of early mechanisms that may lead from obesity towards complications such as metabolic syndrome is of great interest. Here we performed lipidomic analyses of adipose tissue in twin pairs discordant for obesity but still metabolically compensated. In parallel we studied more evolved...... of ethanolamine plasmalogens containing arachidonic acid. Information gathered from these experimental groups was used for molecular dynamics simulations of lipid bilayers combined with dependency network analysis of combined clinical, lipidomics, and gene expression data. The simulations suggested...... also show by in vitro Elovl6 knockdown that the lipid network regulating the observed remodeling may be amenable to genetic modulation. Together, our novel approach suggests a physiological mechanism by which adaptation of adipocyte membranes to adipose tissue expansion associates with positive energy...

  1. The Effects of Temperature and Growth Phase on the Lipidomes of Sulfolobus islandicus and Sulfolobus tokodaii

    DEFF Research Database (Denmark)

    Jensen, Sara Munk; Neesgaard, Vinnie Lund; Skjoldbjerg, Sandra Landbo Nedergaard

    2015-01-01

    at three different temperatures, with samples withdrawn during lag, exponential, and stationary phases. Three abundant tetraether lipid classes and one diether lipid class were monitored. Beside the expected increase in the number of cyclopentane moieties with higher temperature in both archaea, we......The functionality of the plasma membrane is essential for all organisms. Adaption to high growth temperatures imposes challenges and Bacteria, Eukarya, and Archaea have developed several mechanisms to cope with these. Hyperthermophilic archaea have earlier been shown to synthesize tetraether...... membrane lipids with an increased number of cyclopentane moieties at higher growth temperatures. Here we used shotgun lipidomics to study this effect as well as the influence of growth phase on the lipidomes of Sulfolobus islandicus and Sulfolobus tokodaii for the first time. Both species were cultivated...

  2. Complementary Coffee Cups

    Science.gov (United States)

    Banchoff, Thomas

    2006-01-01

    What may have been the birth of a new calculus problem took place when the author noticed that two coffee cups, one convex and one concave, fit nicely together, and he wondered which held more coffee. The fact that their volumes were about equal led to the topic of this article: complementary surfaces of revolution with equal volumes.

  3. Complementary and Integrative Therapies

    Science.gov (United States)

    ... include: • Acupressure and acupuncture • Aromatherapy • Art therapy and music therapy • Chiropractic medicine and massage • Guided imagery • Meditation and ... should I avoid? • Is this complementary therapy (name therapy) safe? Is there research showing it is safe? • Are there side effects ...

  4. Extension of least squares spectral resolution algorithm to high-resolution lipidomics data

    International Nuclear Information System (INIS)

    Zeng, Ying-Xu; Mjøs, Svein Are; David, Fabrice P.A.; Schmid, Adrien W.

    2016-01-01

    Lipidomics, which focuses on the global study of molecular lipids in biological systems, has been driven tremendously by technical advances in mass spectrometry (MS) instrumentation, particularly high-resolution MS. This requires powerful computational tools that handle the high-throughput lipidomics data analysis. To address this issue, a novel computational tool has been developed for the analysis of high-resolution MS data, including the data pretreatment, visualization, automated identification, deconvolution and quantification of lipid species. The algorithm features the customized generation of a lipid compound library and mass spectral library, which covers the major lipid classes such as glycerolipids, glycerophospholipids and sphingolipids. Next, the algorithm performs least squares resolution of spectra and chromatograms based on the theoretical isotope distribution of molecular ions, which enables automated identification and quantification of molecular lipid species. Currently, this methodology supports analysis of both high and low resolution MS as well as liquid chromatography-MS (LC-MS) lipidomics data. The flexibility of the methodology allows it to be expanded to support more lipid classes and more data interpretation functions, making it a promising tool in lipidomic data analysis. - Highlights: • A flexible strategy for analyzing MS and LC-MS data of lipid molecules is proposed. • Isotope distribution spectra of theoretically possible compounds were generated. • High resolution MS and LC-MS data were resolved by least squares spectral resolution. • The method proposed compounds that are likely to occur in the analyzed samples. • The proposed compounds matched results from manual interpretation of fragment spectra.

  5. Extension of least squares spectral resolution algorithm to high-resolution lipidomics data

    Energy Technology Data Exchange (ETDEWEB)

    Zeng, Ying-Xu [Department of Chemistry, University of Bergen, PO Box 7803, N-5020 Bergen (Norway); Mjøs, Svein Are, E-mail: svein.mjos@kj.uib.no [Department of Chemistry, University of Bergen, PO Box 7803, N-5020 Bergen (Norway); David, Fabrice P.A. [Bioinformatics and Biostatistics Core Facility, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL) and Swiss Institute of Bioinformatics (SIB), Lausanne (Switzerland); Schmid, Adrien W. [Proteomics Core Facility, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne (Switzerland)

    2016-03-31

    Lipidomics, which focuses on the global study of molecular lipids in biological systems, has been driven tremendously by technical advances in mass spectrometry (MS) instrumentation, particularly high-resolution MS. This requires powerful computational tools that handle the high-throughput lipidomics data analysis. To address this issue, a novel computational tool has been developed for the analysis of high-resolution MS data, including the data pretreatment, visualization, automated identification, deconvolution and quantification of lipid species. The algorithm features the customized generation of a lipid compound library and mass spectral library, which covers the major lipid classes such as glycerolipids, glycerophospholipids and sphingolipids. Next, the algorithm performs least squares resolution of spectra and chromatograms based on the theoretical isotope distribution of molecular ions, which enables automated identification and quantification of molecular lipid species. Currently, this methodology supports analysis of both high and low resolution MS as well as liquid chromatography-MS (LC-MS) lipidomics data. The flexibility of the methodology allows it to be expanded to support more lipid classes and more data interpretation functions, making it a promising tool in lipidomic data analysis. - Highlights: • A flexible strategy for analyzing MS and LC-MS data of lipid molecules is proposed. • Isotope distribution spectra of theoretically possible compounds were generated. • High resolution MS and LC-MS data were resolved by least squares spectral resolution. • The method proposed compounds that are likely to occur in the analyzed samples. • The proposed compounds matched results from manual interpretation of fragment spectra.

  6. Lipids in host-pathogen interactions: pathogens exploit the complexity of the host cell lipidome.

    Science.gov (United States)

    van der Meer-Janssen, Ynske P M; van Galen, Josse; Batenburg, Joseph J; Helms, J Bernd

    2010-01-01

    Lipids were long believed to have a structural role in biomembranes and a role in energy storage utilizing cellular lipid droplets and plasma lipoproteins. Research over the last decades has identified an additional role of lipids in cellular signaling, membrane microdomain organization and dynamics, and membrane trafficking. These properties make lipids an attractive target for pathogens to modulate host cell processes in order to allow their survival and replication. In this review we will summarize the often ingenious strategies of pathogens to modify the lipid homeostasis of host cells, allowing them to divert cellular processes. To this end pathogens take full advantage of the complexity of the lipidome. The examples are categorized in generalized and emerging principles describing the involvement of lipids in host-pathogen interactions. Several pathogens are described that simultaneously induce multiple changes in the host cell signaling and trafficking mechanisms. Elucidation of these pathogen-induced changes may have important implications for drug development. The emergence of high-throughput lipidomic techniques will allow the description of changes of the host cell lipidome at the level of individual molecular lipid species and the identification of lipid biomarkers.

  7. Alterations in wheat pollen lipidome during high day and night temperature stress.

    Science.gov (United States)

    Narayanan, Sruthi; Prasad, P V Vara; Welti, Ruth

    2018-01-26

    Understanding the adaptive changes in wheat pollen lipidome under high temperature (HT) stress is critical to improving seed set and developing HT tolerant wheat varieties. We measured 89 pollen lipid species under optimum and high day and/or night temperatures using electrospray ionization-tandem mass spectrometry in wheat plants. The pollen lipidome had a distinct composition compared with that of leaves. Unlike in leaves, 34:3 and 36:6 species dominated the composition of extraplastidic phospholipids in pollen under optimum and HT conditions. The most HT-responsive lipids were extraplastidic phospholipids, phosphatidylcholine (PC), phosphatidylethanolamine (PE), phosphatidylinositol, phosphatidic acid, and phosphatidylserine. The unsaturation levels of the extraplastidic phospholipids decreased through the decreases in the levels of 18:3 and increases in the levels of 16:0, 18:0, 18:1, and 18:2 acyl chains. PC and PE were negatively correlated. Higher PC:PE at HT indicated possible PE-to-PC conversion, lower PE formation, or increased PE degradation, relative to PC. Correlation analysis revealed lipids experiencing coordinated metabolism under HT and confirmed the HT responsiveness of extraplastidic phospholipids. Comparison of the present results on wheat pollen with results of our previous research on wheat leaves suggests that similar lipid changes contribute to HT adaptation in both leaves and pollen, though the lipidomes have inherently distinct compositions. © 2018 John Wiley & Sons Ltd.

  8. Bioprospecting of Marine Macrophytes Using MS-Based Lipidomics as a New Approach.

    Science.gov (United States)

    Maciel, Elisabete; Costa Leal, Miguel; Lillebø, Ana Isabel; Domingues, Pedro; Domingues, Maria Rosário; Calado, Ricardo

    2016-03-08

    The marine environment supports a remarkable diversity of organisms which are a potential source of natural products with biological activities. These organisms include a wide variety of marine plants (from micro- to macrophytes), which have been used in the food and pharmaceutical industry. However, the biochemistry and biological activities of many of these macrophytes (namely macroalgae and halophytes, including seagrasses) are still far from being fully explored. Most popular bioactive components include polysaccharides, peptides, phenolics and fatty acids (FAs). Polar lipids (glycolipids, phospholipids and betaine lipids) are emerging as novel value-added bioactive phytochemicals, rich in n-3 FA, with high nutritional value and health beneficial effects for the prevention of chronic diseases. Polar lipids account various combinations of polar groups, fatty acyl chains and backbone structures. The polar lipidome of macrophytes is remarkably diverse, and its screening represents a significant analytical challenge. Modern research platforms, particularly mass spectrometry (MS)-based lipidomic approaches, have been recently used to address this challenge and are here reviewed. The application of lipidomics to address lipid composition of marine macrophytes will contribute to the stimulation of further research on this group and foster the exploration of novel applications.

  9. Bioprospecting of Marine Macrophytes Using MS-Based Lipidomics as a New Approach

    Directory of Open Access Journals (Sweden)

    Elisabete Maciel

    2016-03-01

    Full Text Available The marine environment supports a remarkable diversity of organisms which are a potential source of natural products with biological activities. These organisms include a wide variety of marine plants (from micro- to macrophytes, which have been used in the food and pharmaceutical industry. However, the biochemistry and biological activities of many of these macrophytes (namely macroalgae and halophytes, including seagrasses are still far from being fully explored. Most popular bioactive components include polysaccharides, peptides, phenolics and fatty acids (FAs. Polar lipids (glycolipids, phospholipids and betaine lipids are emerging as novel value-added bioactive phytochemicals, rich in n-3 FA, with high nutritional value and health beneficial effects for the prevention of chronic diseases. Polar lipids account various combinations of polar groups, fatty acyl chains and backbone structures. The polar lipidome of macrophytes is remarkably diverse, and its screening represents a significant analytical challenge. Modern research platforms, particularly mass spectrometry (MS-based lipidomic approaches, have been recently used to address this challenge and are here reviewed. The application of lipidomics to address lipid composition of marine macrophytes will contribute to the stimulation of further research on this group and foster the exploration of novel applications.

  10. Comprehensive identification of age-related lipidome changes in rat amygdala during normal aging.

    Directory of Open Access Journals (Sweden)

    Roman Šmidák

    Full Text Available Brain lipids are integral components of brain structure and function. However, only recent advancements of chromatographic techniques together with mass spectrometry allow comprehensive identification of lipid species in complex brain tissue. Lipid composition varies between the individual areas and the majority of previous reports was focusing on individual lipids rather than a lipidome. Herein, a mass spectrometry-based approach was used to evaluate age-related changes in the lipidome of the rat amygdala obtained from young (3 months and old (20 months males of the Sprague-Dawley rat strain. A total number of 70 lipid species with significantly changed levels between the two animal groups were identified spanning four main lipid classes, i.e. glycerolipids, glycerophospholipids, sphingolipids and sterol lipids. These included phospholipids with pleiotropic brain function, such as derivatives of phosphatidylcholine, phosphatidylserine, and phosphatidylethanolamine. The analysis also revealed significant level changes of phosphatidic acid, diacylglycerol, sphingomyelin and ceramide that directly represent lipid signaling and affect amygdala neuronal activity. The amygdala is a crucial brain region for cognitive functions and former studies on rats and humans showed that this region changes its activity during normal aging. As the information on amygdala lipidome is very limited the results obtained in the present study represent a significant novelty and may contribute to further studies on the role of lipid molecules in age-associated changes of amygdala function.

  11. A Healthy Nordic Diet Alters the Plasma Lipidomic Profile in Adults with Features of Metabolic Syndrome in a Multicenter Randomized Dietary Intervention

    DEFF Research Database (Denmark)

    Lankinen, Maria; Schwab, Ursula; Kolehmainen, Marjukka

    2016-01-01

    Background: A healthy Nordic diet is associated with improvements in cardiometabolic risk factors, but the effect on lipidomic profile is not known. Objective: The aim was to investigate how a healthy Nordic diet affects the fasting plasma lipidomic profile in subjects with metabolic syndrome. Me...

  12. Fibromyalgia and Complementary Health Approaches

    Science.gov (United States)

    ... Musculoskeletal and Skin Diseases Web site . What the Science Says About Complementary Health Approaches for Fibromyalgia Mind ... Complementary and alternative medical therapies in fibromyalgia . Current Pharmaceutical Design . 2006;12(1):47–57. Sherman KJ, ...

  13. Advancing the large-scale CCS database for metabolomics and lipidomics at the machine-learning era.

    Science.gov (United States)

    Zhou, Zhiwei; Tu, Jia; Zhu, Zheng-Jiang

    2018-02-01

    Metabolomics and lipidomics aim to comprehensively measure the dynamic changes of all metabolites and lipids that are present in biological systems. The use of ion mobility-mass spectrometry (IM-MS) for metabolomics and lipidomics has facilitated the separation and the identification of metabolites and lipids in complex biological samples. The collision cross-section (CCS) value derived from IM-MS is a valuable physiochemical property for the unambiguous identification of metabolites and lipids. However, CCS values obtained from experimental measurement and computational modeling are limited available, which significantly restricts the application of IM-MS. In this review, we will discuss the recently developed machine-learning based prediction approach, which could efficiently generate precise CCS databases in a large scale. We will also highlight the applications of CCS databases to support metabolomics and lipidomics. Copyright © 2017 Elsevier Ltd. All rights reserved.

  14. Next-generation transcriptome assembly

    Energy Technology Data Exchange (ETDEWEB)

    Martin, Jeffrey A.; Wang, Zhong

    2011-09-01

    Transcriptomics studies often rely on partial reference transcriptomes that fail to capture the full catalog of transcripts and their variations. Recent advances in sequencing technologies and assembly algorithms have facilitated the reconstruction of the entire transcriptome by deep RNA sequencing (RNA-seq), even without a reference genome. However, transcriptome assembly from billions of RNA-seq reads, which are often very short, poses a significant informatics challenge. This Review summarizes the recent developments in transcriptome assembly approaches - reference-based, de novo and combined strategies-along with some perspectives on transcriptome assembly in the near future.

  15. Associations of the plasma lipidome with mortality in the acute respiratory distress syndrome: a longitudinal cohort study.

    Science.gov (United States)

    Maile, Michael D; Standiford, Theodore J; Engoren, Milo C; Stringer, Kathleen A; Jewell, Elizabeth S; Rajendiran, Thekkelnaycke M; Soni, Tanu; Burant, Charles F

    2018-04-10

    It is unknown if the plasma lipidome is a useful tool for improving our understanding of the acute respiratory distress syndrome (ARDS). Therefore, we measured the plasma lipidome of individuals with ARDS at two time-points to determine if changes in the plasma lipidome distinguished survivors from non-survivors. We hypothesized that both the absolute concentration and change in concentration over time of plasma lipids are associated with 28-day mortality in this population. Samples for this longitudinal observational cohort study were collected at multiple tertiary-care academic medical centers as part of a previous multicenter clinical trial. A mass spectrometry shot-gun lipidomic assay was used to quantify the lipidome in plasma samples from 30 individuals. Samples from two different days were analyzed for each subject. After removing lipids with a coefficient of variation > 30%, differences between cohorts were identified using repeated measures analysis of variance. The false discovery rate was used to adjust for multiple comparisons. Relationships between significant compounds were explored using hierarchical clustering of the Pearson correlation coefficients and the magnitude of these relationships was described using receiver operating characteristic curves. The mass spectrometry assay reliably measured 359 lipids. After adjusting for multiple comparisons, 90 compounds differed between survivors and non-survivors. Survivors had higher levels for each of these lipids except for five membrane lipids. Glycerolipids, particularly those containing polyunsaturated fatty acid side-chains, represented many of the lipids with higher concentrations in survivors. The change in lipid concentration over time did not differ between survivors and non-survivors. The concentration of multiple plasma lipids is associated with mortality in this group of critically ill patients with ARDS. Absolute lipid levels provided more information than the change in concentration over

  16. Lipidomic analysis of biological samples: Comparison of liquid chromatography, supercritical fluid chromatography and direct infusion mass spectrometry methods.

    Science.gov (United States)

    Lísa, Miroslav; Cífková, Eva; Khalikova, Maria; Ovčačíková, Magdaléna; Holčapek, Michal

    2017-11-24

    Lipidomic analysis of biological samples in a clinical research represents challenging task for analytical methods given by the large number of samples and their extreme complexity. In this work, we compare direct infusion (DI) and chromatography - mass spectrometry (MS) lipidomic approaches represented by three analytical methods in terms of comprehensiveness, sample throughput, and validation results for the lipidomic analysis of biological samples represented by tumor tissue, surrounding normal tissue, plasma, and erythrocytes of kidney cancer patients. Methods are compared in one laboratory using the identical analytical protocol to ensure comparable conditions. Ultrahigh-performance liquid chromatography/MS (UHPLC/MS) method in hydrophilic interaction liquid chromatography mode and DI-MS method are used for this comparison as the most widely used methods for the lipidomic analysis together with ultrahigh-performance supercritical fluid chromatography/MS (UHPSFC/MS) method showing promising results in metabolomics analyses. The nontargeted analysis of pooled samples is performed using all tested methods and 610 lipid species within 23 lipid classes are identified. DI method provides the most comprehensive results due to identification of some polar lipid classes, which are not identified by UHPLC and UHPSFC methods. On the other hand, UHPSFC method provides an excellent sensitivity for less polar lipid classes and the highest sample throughput within 10min method time. The sample consumption of DI method is 125 times higher than for other methods, while only 40μL of organic solvent is used for one sample analysis compared to 3.5mL and 4.9mL in case of UHPLC and UHPSFC methods, respectively. Methods are validated for the quantitative lipidomic analysis of plasma samples with one internal standard for each lipid class. Results show applicability of all tested methods for the lipidomic analysis of biological samples depending on the analysis requirements

  17. Lipidomic changes in rat liver after long-term exposure to ethanol

    International Nuclear Information System (INIS)

    Fernando, Harshica; Bhopale, Kamlesh K.; Kondraganti, Shakuntala; Kaphalia, Bhupendra S.; Shakeel Ansari, G.A.

    2011-01-01

    Alcoholic liver disease (ALD) is a serious health problem with significant morbidity and mortality. In this study we examined the progression of ALD along with lipidomic changes in rats fed ethanol for 2 and 3 months to understand the mechanism, and identify possible biomarkers. Male Fischer 344 rats were fed 5% ethanol or caloric equivalent of maltose-dextrin in a Lieber-DeCarli diet. Animals were killed at the end of 2 and 3 months and plasma and livers were collected. Portions of the liver were fixed for histological and immunohistological studies. Plasma and the liver lipids were extracted and analyzed by nuclear magnetic resonance (NMR) spectroscopy. A time dependent fatty infiltration was observed in the livers of ethanol-fed rats. Mild inflammation and oxidative stress were observed in some ethanol-fed rats at 3 months. The multivariate and principal component analysis of proton and phosphorus NMR spectroscopy data of extracted lipids from the plasma and livers showed segregation of ethanol-fed groups from the pair-fed controls. Significant hepatic lipids that were increased by ethanol exposure included fatty acids and triglycerides, whereas phosphatidylcholine (PC) decreased. However, both free fatty acids and PC decreased in the plasma. In liver lipids unsaturation of fatty acyl chains increased, contrary to plasma, where it decreased. Our studies confirm that over-accumulation of lipids in ethanol-induced liver steatosis accompanied by mild inflammation on long duration of ethanol exposure. Identified metabolic profile using NMR lipidomics could be further explored to establish biomarker signatures representing the etiopathogenesis, progression and/or severity of ALD. - Highlights: → Long term exposure to ethanol was studied. → A nuclear magnetic resonance (NMR) spectroscopy based lipidomic approach was used. → We examined the clustering pattern of the NMR data with principal component analysis. → NMR data were compared with histology and

  18. High-resolution proteomic and lipidomic analysis of exosomes and microvesicles from different cell sources

    Directory of Open Access Journals (Sweden)

    Reka A. Haraszti

    2016-11-01

    Full Text Available Extracellular vesicles (EVs, including exosomes and microvesicles (MVs, are explored for use in diagnostics, therapeutics and drug delivery. However, little is known about the relationship of protein and lipid composition of EVs and their source cells. Here, we report high-resolution lipidomic and proteomic analyses of exosomes and MVs derived by differential ultracentrifugation from 3 different cell types: U87 glioblastoma cells, Huh7 hepatocellular carcinoma cells and human bone marrow-derived mesenchymal stem cells (MSCs. We identified 3,532 proteins and 1,961 lipid species in the screen. Exosomes differed from MVs in several different areas: (a The protein patterns of exosomes were more likely different from their cells of origin than were the protein patterns of MVs; (b The proteomes of U87 and Huh7 exosomes were similar to each other but different from the proteomes of MSC exosomes, whereas the lipidomes of Huh7 and MSC exosomes were similar to each other but different from the lipidomes of U87 exosomes; (c exosomes exhibited proteins of extracellular matrix, heparin-binding, receptors, immune response and cell adhesion functions, whereas MVs were enriched in endoplasmic reticulum, proteasome and mitochondrial proteins. Exosomes and MVs also differed in their types of lipid contents. Enrichment in glycolipids and free fatty acids characterized exosomes, whereas enrichment in ceramides and sphingomyelins characterized MVs. Furthermore, Huh7 and MSC exosomes were specifically enriched in cardiolipins; U87 exosomes were enriched in sphingomyelins. This study comprehensively analyses the protein and lipid composition of exosomes, MVs and source cells in 3 different cell types.

  19. Dysregulation of soluble epoxide hydrolase and lipidomic profiles in anorexia nervosa

    KAUST Repository

    Shih, P. B.

    2015-03-31

    Individuals with anorexia nervosa (AN) restrict eating and become emaciated. They tend to have an aversion to foods rich in fat. Because epoxide hydrolase 2 (EPHX2) was identified as a novel AN susceptibility gene, and because its protein product, soluble epoxide hydrolase (sEH), converts bioactive epoxides of polyunsaturated fatty acid (PUFA) to the corresponding diols, lipidomic and metabolomic targets of EPHX2 were assessed to evaluate the biological functions of EPHX2 and their role in AN. Epoxide substrates of sEH and associated oxylipins were measured in ill AN, recovered AN and gender- and race-matched controls. PUFA and oxylipin markers were tested as potential biomarkers for AN. Oxylipin ratios were calculated as proxy markers of in vivo sEH activity. Several free- and total PUFAs were associated with AN diagnosis and with AN recovery. AN displayed elevated n-3 PUFAs and may differ from controls in PUFA elongation and desaturation processes. Cytochrome P450 pathway oxylipins from arachidonic acid, linoleic acid, alpha-linolenic acid and docosahexaenoic acid PUFAs are associated with AN diagnosis. The diol:epoxide ratios suggest the sEH activity is higher in AN compared with controls. Multivariate analysis illustrates normalization of lipidomic profiles in recovered ANs. EPHX2 influences AN risk through in vivo interaction with dietary PUFAs. PUFA composition and concentrations as well as sEH activity may contribute to the pathogenesis and prognosis of AN. Our data support the involvement of EPHX2-associated lipidomic and oxylipin dysregulations in AN, and reveal their potential as biomarkers to assess responsiveness to future intervention or treatment.

  20. Lipidomic analysis of two closely related strains of the microalga Parietochloris (Trebouxiophyceae, Chlorophyta)

    Czech Academy of Sciences Publication Activity Database

    Řezanka, Tomáš; Nedbalová, Linda; Lukavský, Jaromír; Procházková, L.; Sigler, Karel

    2017-01-01

    Roč. 25, JUL 2017 (2017), s. 473-482 ISSN 2211-9264 R&D Projects: GA ČR(CZ) GA17-00027S Institutional support: RVO:61388971 ; RVO:67985939 Keywords : Parietochloris * Arachidonic acid * Lipidomics Subject RIV: EE - Microbiology, Virology; EI - Biotechnology ; Bionics (BU-J) OBOR OECD: Microbiology; Bioproducts (products that are manufactured using biological material as feedstock) biomaterials, bioplastics, biofuels, bioderived bulk and fine chemicals, bio-derived novel materials (BU-J) Impact factor: 3.994, year: 2016

  1. A complementary MOS process

    International Nuclear Information System (INIS)

    Jhabvala, M.D.

    1977-03-01

    The complete sequence used to manufacture complementary metal oxide semiconductor (CMOS) integrated circuits is described. The fixed-gate array concept is presented as a means of obtaining CMOS integrated circuits in a fast and reliable fashion. Examples of CMOS circuits fabricated by both the conventional method and the fixed-gate array method are included. The electrical parameter specifications and characteristics are given along with typical values used to produce CMOS circuits. Temperature-bias stressing data illustrating the thermal stability of devices manufactured by this process are presented. Results of a preliminary study on the radiation sensitivity of circuits manufactured by this process are discussed. Some process modifications are given which have improved the radiation hardness of our CMOS devices. A formula description of the chemicals and gases along with the gas flow rates is also included

  2. Evidence of a DHA Signature in the Lipidome and Metabolome of Human Hepatocytes

    Directory of Open Access Journals (Sweden)

    Veronica Ghini

    2017-02-01

    Full Text Available Cell supplementation with bioactive molecules often causes a perturbation in the whole intracellular environment. Omics techniques can be applied for the assessment of this perturbation. In this study, the overall effect of docosahexaenoic acid (DHA supplementation on cultured human hepatocyte lipidome and metabolome has been investigated using nuclear magnetic resonance (NMR in combination with traditional techniques. The effect of two additional bioactives sharing with DHA the lipid-lowering effect—propionic acid (PRO and protocatechuic acid (PCA—has also been evaluated in the context of possible synergism. NMR analysis of the cell lipid extracts showed that DHA supplementation, alone or in combination with PCA or PRO, strongly altered the cell lipid profile. The perfect discrimination between cells receiving DHA (alone or in combination and the other cells reinforced the idea of a global rearrangement of the lipid environment induced by DHA. Notably, gas chromatography and fluorimetric analyses confirmed the strong discrimination obtained by NMR. The DHA signature was evidenced not only in the cell lipidome, but also in the metabolome. Results reported herein indicate that NMR, combined with other techniques, represents a fundamental approach to studying the effect of bioactive supplementation, particularly in the case of molecules with a broad spectrum of mechanisms of action.

  3. Lipidomic Approaches towards Deciphering Glycolipids from Microalgae as a Reservoir of Bioactive Lipids

    Directory of Open Access Journals (Sweden)

    Elisabete da Costa

    2016-05-01

    Full Text Available In recent years, noteworthy research has been performed around lipids from microalgae. Among lipids, glycolipids (GLs are quite abundant in microalgae and are considered an important source of fatty acids (FAs. GLs are rich in 16- and 18-carbon saturated and unsaturated fatty acids and often contain polyunsaturated fatty acids (PUFAs like n-3 α-linolenic (ALA 18:3, eicosapentaenoic (EPA, 20:5 and docosahexaenoic (DHA, 22:6. GLs comprise three major classes: monogalactosyldiacyl glycerolipids (MGDGs, digalactosyl diacylglycerolipids (DGDGs and sulfoquinovosyl diacylglycerolipids (SQDGs, whose composition in FA directly depends on the growth conditions. Some of these lipids are high value-added compounds with antitumoral, antimicrobial and anti-inflammatory activities and also with important nutritional significance. To fully explore GLs’ bioactive properties it is necessary to fully characterize their structure and to understand the relation between the structure and their biological properties, which can be addressed using modern mass spectrometry (MS-based lipidomic approaches. This review will focus on the up-to-date FA composition of GLs identified by MS-based lipidomics and their potential as phytochemicals.

  4. The application of lipidomics to biomarker research and pathomechanisms in Alzheimer's disease.

    Science.gov (United States)

    Wong, Matthew W; Braidy, Nady; Poljak, Anne; Sachdev, Perminder S

    2017-03-01

    Alzheimer's disease is the most common cause of dementia. There are still no disease modifying treatments that can cure or slow disease progression. Recently, Alzheimer's disease researchers have attempted to improve early detection and diagnostic criteria for Alzheimer's disease, with the rationale that treatment of disease, or even prevention, may be more successful during the early preclinical stages of Alzheimer's disease when neurodegenerative damage is not as widespread. As the brain has a high lipid content, lipidomics may offer novel insights into the underlying pathogenesis of Alzheimer's disease. This review reports on recent developments in the relatively unexplored field of lipidomics in Alzheimer's disease, including novel biomarkers and pathomechanisms of Alzheimer's disease. Numerous biomarker panels involving phospholipids and sphingolipids have been proposed, indicating perturbed lipid metabolism in early stages of Alzheimer's disease. Future strategies targeting these metabolic changes through dietary supplementation could have therapeutic benefits in at-risk individuals. Dysregulated lipid metabolism could reflect pathological changes in synaptic function and neuronal membranes, leading to cognitive decline. However, extensive validation in large independent cohorts is required before lipid biomarkers can be used clinically to assess Alzheimer's disease risk and progression.

  5. Correlated Heterospectral Lipidomics for Biomolecular Profiling of Remyelination in Multiple Sclerosis

    Directory of Open Access Journals (Sweden)

    Mads S. Bergholt

    2017-12-01

    Full Text Available Analyzing lipid composition and distribution within the brain is important to study white matter pathologies that present focal demyelination lesions, such as multiple sclerosis. Some lesions can endogenously re-form myelin sheaths. Therapies aim to enhance this repair process in order to reduce neurodegeneration and disability progression in patients. In this context, a lipidomic analysis providing both precise molecular classification and well-defined localization is crucial to detect changes in myelin lipid content. Here we develop a correlated heterospectral lipidomic (HSL approach based on coregistered Raman spectroscopy, desorption electrospray ionization mass spectrometry (DESI-MS, and immunofluorescence imaging. We employ HSL to study the structural and compositional lipid profile of demyelination and remyelination in an induced focal demyelination mouse model and in multiple sclerosis lesions from patients ex vivo. Pixelwise coregistration of Raman spectroscopy and DESI-MS imaging generated a heterospectral map used to interrelate biomolecular structure and composition of myelin. Multivariate regression analysis enabled Raman-based assessment of highly specific lipid subtypes in complex tissue for the first time. This method revealed the temporal dynamics of remyelination and provided the first indication that newly formed myelin has a different lipid composition compared to normal myelin. HSL enables detailed molecular myelin characterization that can substantially improve upon the current understanding of remyelination in multiple sclerosis and provides a strategy to assess remyelination treatments in animal models.

  6. Nutrition and Reproductive Health: Sperm versus Erythrocyte Lipidomic Profile and ω-3 Intake

    Directory of Open Access Journals (Sweden)

    Gabriela Ruth Mendeluk

    2015-01-01

    Full Text Available Fatty acid analyses of sperm and erythrocyte cell membrane phospholipids in idiopathic infertile patients evidenced that erythrocyte contents of EPA, DHA, omega-6–omega-3 ratio and arachidonic acid provide a mathematical correspondence for the prediction of EPA level in sperm cells. The erythrocyte lipidomic profile of patients was significantly altered, with signatures of typical Western pattern dietary habits and no fish intake. A supplementation with nutritional levels of EPA and DHA and antioxidants was then performed for 3 months, with the follow-up of both erythrocyte and sperm cell membranes composition as well as conventional sperm parameters. Some significant changes were found in the lipidomic membrane profile of erythrocyte but not in sperm cells, which correspondently did not show significant parameter ameliorations. This is the first report indicating that membrane lipids of different tissues do not equally metabolize the fatty acid elements upon supplementation. Molecular diagnostic tools are necessary to understand the cell metabolic turnover and monitor the success of nutraceuticals for personalized treatments.

  7. Association of lipidome remodeling in the adipocyte membrane with acquired obesity in humans.

    Directory of Open Access Journals (Sweden)

    Kirsi H Pietiläinen

    2011-06-01

    Full Text Available Identification of early mechanisms that may lead from obesity towards complications such as metabolic syndrome is of great interest. Here we performed lipidomic analyses of adipose tissue in twin pairs discordant for obesity but still metabolically compensated. In parallel we studied more evolved states of obesity by investigating a separated set of individuals considered to be morbidly obese. Despite lower dietary polyunsaturated fatty acid intake, the obese twin individuals had increased proportions of palmitoleic and arachidonic acids in their adipose tissue, including increased levels of ethanolamine plasmalogens containing arachidonic acid. Information gathered from these experimental groups was used for molecular dynamics simulations of lipid bilayers combined with dependency network analysis of combined clinical, lipidomics, and gene expression data. The simulations suggested that the observed lipid remodeling maintains the biophysical properties of lipid membranes, at the price, however, of increasing their vulnerability to inflammation. Conversely, in morbidly obese subjects, the proportion of plasmalogens containing arachidonic acid in the adipose tissue was markedly decreased. We also show by in vitro Elovl6 knockdown that the lipid network regulating the observed remodeling may be amenable to genetic modulation. Together, our novel approach suggests a physiological mechanism by which adaptation of adipocyte membranes to adipose tissue expansion associates with positive energy balance, potentially leading to higher vulnerability to inflammation in acquired obesity. Further studies will be needed to determine the cause of this effect.

  8. Comparative Lipidomic Analysis of Mouse and Human Brain with Alzheimer Disease*

    Science.gov (United States)

    Chan, Robin B.; Oliveira, Tiago G.; Cortes, Etty P.; Honig, Lawrence S.; Duff, Karen E.; Small, Scott A.; Wenk, Markus R.; Shui, Guanghou; Di Paolo, Gilbert

    2012-01-01

    Lipids are key regulators of brain function and have been increasingly implicated in neurodegenerative disorders including Alzheimer disease (AD). Here, a systems-based approach was employed to determine the lipidome of brain tissues affected by AD. Specifically, we used liquid chromatography-mass spectrometry to profile extracts from the prefrontal cortex, entorhinal cortex, and cerebellum of late-onset AD (LOAD) patients, as well as the forebrain of three transgenic familial AD (FAD) mouse models. Although the cerebellum lacked major alterations in lipid composition, we found an elevation of a signaling pool of diacylglycerol as well as sphingolipids in the prefrontal cortex of AD patients. Furthermore, the diseased entorhinal cortex showed specific enrichment of lysobisphosphatidic acid, sphingomyelin, the ganglioside GM3, and cholesterol esters, all of which suggest common pathogenic mechanisms associated with endolysosomal storage disorders. Importantly, a significant increase in cholesterol esters and GM3 was recapitulated in the transgenic FAD models, suggesting that these mice are relevant tools to study aberrant lipid metabolism of endolysosomal dysfunction associated with AD. Finally, genetic ablation of phospholipase D2, which rescues the synaptic and behavioral deficits of an FAD mouse model, fully normalizes GM3 levels. These data thus unmask a cross-talk between the metabolism of phosphatidic acid, the product of phospholipase D2, and gangliosides, and point to a central role of ganglioside anomalies in AD pathogenesis. Overall, our study highlights the hypothesis generating potential of lipidomics and identifies novel region-specific lipid anomalies potentially linked to AD pathogenesis. PMID:22134919

  9. Stereoselective bioaccumulation of chiral PCB 91 in earthworm and its metabolomic and lipidomic responses.

    Science.gov (United States)

    He, Zeying; Wang, Yuehua; Zhang, Yanwei; Cheng, Haiyan; Liu, Xiaowei

    2018-07-01

    Stereoselective bioaccumulation, elimination, metabolomic and lipidomic responses of earthworm Eisenia fetida exposed to chiral polychlorinated biphenyl (PCB) 91 in an earthworm-soil system were investigated. Preferential bioaccumulation of (-)-PCB 91 and elimination of (+)-PCB 91 were observed following 50 and 500 μg/kg dwt exposures. Enantiomer fraction (EF) values decreased over time during the uptake and elimination periods. Metabolomics and lipidomics techniques based on ultra-performance liquid chromatography/quadrupole time-of-flight mass spectrometry (UPLC-QTOF-MS) revealed significant changes in 108 metabolites after earthworms exposure to (+)-, (-)-, and (±)-PCB 91, compared to control groups. Forty two of these metabolites were identified as amino acids, nucleosides, fatty acids, dicarboxylic acids, vitamins or others. Lysophospholipids including six lysophosphatidylcholines (LPC), six lysophosphatidylethanolamine (LPE), eight lysophosphatidylinositol (LPI) and five lysophosphatidylserine (LPS) were also differentially expressed between exposure and control groups. Alterations in the levels of metabolites and lipids indicated stereoselective effects of chiral PCB 91 on earthworm amino acid, energy, and nucleotide metabolism, neurodevelopment and gene expression. Overall, the effects of (+)-PCB 91 were more pronounced than that of (-)- and (±)-PCB 91. Copyright © 2018 Elsevier Ltd. All rights reserved.

  10. The lipidome, genotoxicity, hematotoxicity and antioxidant properties of andiroba oil from the Brazilian Amazon

    Directory of Open Access Journals (Sweden)

    Susana Suely Rodrigues Milhomem-Paixão

    2016-01-01

    Full Text Available Abstract Andirobeira is an Amazonian tree, the seeds of which produce a commercially valuable oil that is used in folk medicine and in the cosmetic industry. Andiroba oil contains components with anti-inflammatory, cicatrizing and insect-repellant actions. However, virtually nothing is known of the safety of this oil for humans. The aim of this work was therefore to investigate the hematotoxicity, genotoxicity and mutagenicity of andiroba oil using the comet and micronucleus assays, and to assess its antioxidant properties and lipidome as a means of addressing safety issues. For the experiments, andiroba oil was administered by gavage for 14 consecutive days in nulliparous female Swiss mice randomly distributed in four groups: negative control and three doses of oil (500, 1000 and 2000 mg/kg/day. These doses were chosen based on recommendations of the OECD guideline no. 474 (1997. GC/MS was used to investigate the free fatty acid, cholesterol and triterpene content of andiroba oil in a lipidomic analysis. No clinical or behavioral alterations were observed throughout the period of treatment, and exposure to andiroba oil at the doses and conditions used here did not result in hematotoxic, genotoxic or mutagenic effects. Tests in vitro showed that oil sample 3 from southwestern of Brazilian Amazon had a high antioxidant capacity that may protect biological systems from oxidative stress, although this activity remains to be demonstrated in vivo.

  11. Lipidome and metabolome analysis of fresh tobacco leaves in different geographical regions using liquid chromatography-mass spectrometry.

    Science.gov (United States)

    Li, Lili; Lu, Xin; Zhao, Jieyu; Zhang, Junjie; Zhao, Yanni; Zhao, Chunxia; Xu, Guowang

    2015-07-01

    The combination of the lipidome and the metabolome can provide much more information in plant metabolomics studies. A method for the simultaneous extraction of the lipidome and the metabolome of fresh tobacco leaves was developed. Method validation was performed on the basis of the optimal ratio of methanol to methyl tert-butyl ether to water (37:45:68) from the design of experiments. Good repeatability was obtained. We found that 92.2% and 91.6% of the peaks for the lipidome and the metabolome were within a relative standard deviation of 20%, accounting for 94.6% and 94.6% of the total abundance, respectively. The intraday and interday precisions were also satisfactory. A total of 230 metabolites, including 129 lipids, were identified. Significant differences were found in lipidomic and metabolomic profiles of fresh tobacco leaves in different geographical regions. Highly unsaturated galactolipids, phosphatidylethanolamines, predominant phosphatidylcholines, most of the polyphenols, amino acids, and polyamines had a higher content in Yunnan province, and low-unsaturation-degree galactolipids, triacylglycerols, glucosylceramides with trihydroxy long-chain bases, acylated sterol glucosides, and some organic acids were more abundant in Henan province. Correlation analysis between differential metabolites and climatic factors indicated the vital importance of temperature. The fatty acid unsaturation degree of galactolipids could be influenced by temperature. Accumulation of polyphenols and decreases in the ratios of stigmasterols to sitosterols and glucosylstigmasterols to glucosylsitosterols were also correlated with lower temperature in Yunnan province. Furthermore, lipids were more sensitive to climatic variations than other metabolites.

  12. Effects of the BET-inhibitor, RVX-208 on the HDL lipidome and glucose metabolism in individuals with prediabetes

    DEFF Research Database (Denmark)

    Siebel, Andrew L; Trinh, Si Khiang; Formosa, Melissa F

    2016-01-01

    (HDL lipidome) and glucose metabolism. MATERIALS AND METHODS: Twenty unmedicated males with prediabetes received 100mg b.i.d. RVX-208 and placebo for 29-33days separated by a wash-out period in a randomized, cross-over design trial. Plasma HDL-cholesterol and apoA-I were assessed as well as lipoprotein...

  13. Transmuted Complementary Weibull Geometric Distribution

    Directory of Open Access Journals (Sweden)

    Ahmed Z. A…fify

    2014-12-01

    Full Text Available This paper provides a new generalization of the complementary Weibull geometric distribution that introduced by Tojeiro et al. (2014, using the quadratic rank transmutation map studied by Shaw and Buckley (2007. The new distribution is referred to as transmuted complementary Weibull geometric distribution (TCWGD. The TCWG distribution includes as special cases the complementary Weibull geometric distribution (CWGD, complementary exponential geometric distribution(CEGD,Weibull distribution (WD and exponential distribution (ED. Various structural properties of the new distribution including moments, quantiles, moment generating function and RØnyi entropy of the subject distribution are derived. We proposed the method of maximum likelihood for estimating the model parameters and obtain the observed information matrix. A real data set are used to compare the ‡exibility of the transmuted version versus the complementary Weibull geometric distribution.

  14. Detection of Independent Associations of Plasma Lipidomic Parameters with Insulin Sensitivity Indices Using Data Mining Methodology.

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    Steffi Kopprasch

    Full Text Available Glucolipotoxicity is a major pathophysiological mechanism in the development of insulin resistance and type 2 diabetes mellitus (T2D. We aimed to detect subtle changes in the circulating lipid profile by shotgun lipidomics analyses and to associate them with four different insulin sensitivity indices.The cross-sectional study comprised 90 men with a broad range of insulin sensitivity including normal glucose tolerance (NGT, n = 33, impaired glucose tolerance (IGT, n = 32 and newly detected T2D (n = 25. Prior to oral glucose challenge plasma was obtained and quantitatively analyzed for 198 lipid molecular species from 13 different lipid classes including triacylglycerls (TAGs, phosphatidylcholine plasmalogen/ether (PC O-s, sphingomyelins (SMs, and lysophosphatidylcholines (LPCs. To identify a lipidomic signature of individual insulin sensitivity we applied three data mining approaches, namely least absolute shrinkage and selection operator (LASSO, Support Vector Regression (SVR and Random Forests (RF for the following insulin sensitivity indices: homeostasis model of insulin resistance (HOMA-IR, glucose insulin sensitivity index (GSI, insulin sensitivity index (ISI, and disposition index (DI. The LASSO procedure offers a high prediction accuracy and and an easier interpretability than SVR and RF.After LASSO selection, the plasma lipidome explained 3% (DI to maximal 53% (HOMA-IR variability of the sensitivity indexes. Among the lipid species with the highest positive LASSO regression coefficient were TAG 54:2 (HOMA-IR, PC O- 32:0 (GSI, and SM 40:3:1 (ISI. The highest negative regression coefficient was obtained for LPC 22:5 (HOMA-IR, TAG 51:1 (GSI, and TAG 58:6 (ISI.Although a substantial part of lipid molecular species showed a significant correlation with insulin sensitivity indices we were able to identify a limited number of lipid metabolites of particular importance based on the LASSO approach. These few selected lipids with the closest

  15. High-Resolution Lipidomics of the Early Life Stages of the Red Seaweed Porphyra dioica.

    Science.gov (United States)

    da Costa, Elisabete; Azevedo, Vitor; Melo, Tânia; Rego, Andreia M; V Evtuguin, Dmitry; Domingues, Pedro; Calado, Ricardo; Pereira, Rui; Abreu, Maria H; Domingues, Maria R

    2018-01-17

    Porphyra dioica is a commercial seaweed consumed all over the world, mostly in the shape of nori sheets used for "sushi" preparation. It is a well-known part of the Asian diet with health benefits, which have been associated, among others, to the high levels of n -3 and n- 6 fatty acids in this red alga. However, other highly valued lipids of Porphyra are polar lipids that remain largely undescribed and can have both nutritional value and bioactivity, thus could contribute to the valorization of this seaweed. In this context, the present work aims to identify the lipidome of two life cycle stages of the Atlantic species Porphyra dioica : the early life stage conchocelis produced in an indoor-nursery, and young blades produced outdoors using an integrated multitrophic aquaculture (IMTA) framework. Both the blades (gametophyte) and conchocelis (sporophyte) are commercialized in the food and cosmetics sectors. Liquid chromatography coupled to Q-Exactive high resolution-mass spectrometry (MS) platform was used to gain insight into the lipidome of these species. Our results allowed the identification of 110 and 100 lipid molecular species in the lipidome of the blade and conchocelis, respectively. These lipid molecular species were distributed as follows (blade/conchocelis): 14/15 glycolipids (GLs), 93/79 phospholipids (PLs), and 3/6 betaine lipids. Both life stages displayed a similar profile of GLs and comprised 20:4( n -6) and 20:5( n -3) fatty acids that contribute to n -3 and n -6 fatty acid pool recorded and rank among the molecular species with higher potential bioactivity. PLs' profile was different between the two life stages surveyed, mainly due to the number and relative abundance of molecular species. This finding suggests that differences between both life stages were more likely related with shifts in the lipids of extraplastidial membranes rather than in plastidial membranes. PLs contained n -6 and n -3 precursors and in both life stages of Porphyra

  16. High-Resolution Lipidomics of the Early Life Stages of the Red Seaweed Porphyra dioica

    Directory of Open Access Journals (Sweden)

    Elisabete da Costa

    2018-01-01

    Full Text Available Porphyra dioica is a commercial seaweed consumed all over the world, mostly in the shape of nori sheets used for “sushi” preparation. It is a well-known part of the Asian diet with health benefits, which have been associated, among others, to the high levels of n-3 and n-6 fatty acids in this red alga. However, other highly valued lipids of Porphyra are polar lipids that remain largely undescribed and can have both nutritional value and bioactivity, thus could contribute to the valorization of this seaweed. In this context, the present work aims to identify the lipidome of two life cycle stages of the Atlantic species Porphyra dioica: the early life stage conchocelis produced in an indoor-nursery, and young blades produced outdoors using an integrated multitrophic aquaculture (IMTA framework. Both the blades (gametophyte and conchocelis (sporophyte are commercialized in the food and cosmetics sectors. Liquid chromatography coupled to Q–Exactive high resolution-mass spectrometry (MS platform was used to gain insight into the lipidome of these species. Our results allowed the identification of 110 and 100 lipid molecular species in the lipidome of the blade and conchocelis, respectively. These lipid molecular species were distributed as follows (blade/conchocelis: 14/15 glycolipids (GLs, 93/79 phospholipids (PLs, and 3/6 betaine lipids. Both life stages displayed a similar profile of GLs and comprised 20:4(n-6 and 20:5(n-3 fatty acids that contribute to n-3 and n-6 fatty acid pool recorded and rank among the molecular species with higher potential bioactivity. PLs’ profile was different between the two life stages surveyed, mainly due to the number and relative abundance of molecular species. This finding suggests that differences between both life stages were more likely related with shifts in the lipids of extraplastidial membranes rather than in plastidial membranes. PLs contained n-6 and n-3 precursors and in both life stages of

  17. Assessment of potential false positives via orbitrap-based untargeted lipidomics from rat tissues.

    Science.gov (United States)

    Xu, Lina; Wang, Xueying; Jiao, Yupei; Liu, Xiaohui

    2018-02-01

    Untargeted lipidomics is increasingly popular due to the broad coverage of lipid species. Data dependent MS/MS acquisition is commonly used in order to acquire sufficient information for confident lipid assignment. However, although lipids are identified based on MS/MS confirmation, a number of false positives are still observed. Here, we discuss several causes of introducing lipid false identifications in untargeted analysis. Phosphotidylcholines and cholesteryl esters generate in-source fragmentation to produce dimethylated phosphotidylethanolamine and free cholesterol. Dimerization of fatty acid results in false identification of fatty acid ester of hydroxyl fatty acid. Realizing these false positives is able to improve confidence of results acquired from untargeted analysis. Besides, thresholds are established for lipids identified using LipidSearch v4.1.16 software to reduce unreliable results. Copyright © 2017 Elsevier B.V. All rights reserved.

  18. TLC-Blot (Far-Eastern Blot) and Its Application to Functional Lipidomics.

    Science.gov (United States)

    Taki, Takao

    2015-01-01

    A simple method for transfer of lipids-including phospholipids, glycolipids, and neutral lipids-from a high performance thin layer chromatography (HPTLC) plate to a polyvinylidene difluoride (PVDF) membrane, TLC-Blot (Far-Eastern Blot), and its biochemical applications are presented. This chapter presents the conventional procedures for separating lipid from tissue samples, cultured cells, and serum and the subsequent development of TLC. Individual lipids separated on an HPTLC plate can be transferred to the PVDF membrane quantitatively and also isolated from the lipid-blotted membrane by a one-step purification procedure. Immunodetection with monoclonal antibodies and treatment with lipid-metabolizing enzymes on the lipid-blotted membrane are possible. The method for identification of individual lipids transferred on the PVDF membrane using matrix-assisted laser desorption/ionization quadrupole ion trap time-of-flight mass spectrometry (TLC-Blot/MALDI-TOF MS) is shown as a functional lipidomics application.

  19. Zebrafish Embryonic Lipidomic Analysis Reveals that the Yolk Cell Is Metabolically Active in Processing Lipid

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    Daniel Fraher

    2016-02-01

    Full Text Available The role of lipids in providing energy and structural cellular components during vertebrate development is poorly understood. To elucidate these roles further, we visualized lipid deposition and examined expression of key lipid-regulating genes during zebrafish embryogenesis. We also conducted a semiquantitative analysis of lipidomic composition using liquid chromatography (LC-mass spectrometry. Finally, we analyzed processing of boron-dipyrromethene (BODIPY lipid analogs injected into the yolk using thin layer chromatography. Our data reveal that the most abundant lipids in the embryo are cholesterol, phosphatidylcholine, and triglyceride. Moreover, we demonstrate that lipids are processed within the yolk prior to mobilization to the embryonic body. Our data identify a metabolically active yolk and body resulting in a dynamic lipid composition. This provides a foundation for studying lipid biology during normal or pharmacologically compromised embryogenesis.

  20. Life — As a Matter of Fat The Emerging Science of Lipidomics

    CERN Document Server

    Mouritsen, Ole G

    2005-01-01

    LIFE - as a Matter of Fat Lipidomics is the science of the fats called lipids. Lipids are as important for life as proteins, sugars, and genes. The present book gives a multi-disciplinary perspective on the physics of life and the particular role played by lipids and the lipid-bilayer component of cell membranes. The book is aimed at undergraduate students and young research workers within physics, chemistry, biochemistry, molecular biology, nutrition, as well as pharmaceutical and biomedical sciences. The emphasis is on the physical properties of lipid membranes seen as soft and molecularly structured interfaces. By combining and synthesizing insights obtained from a variety of recent studies, an attempt is made to clarify what membrane structure is and how it can be quantitatively described. Furthermore, it is shown how biological function mediated by membranes is controlled by lipid membrane structure and organization on length scales ranging from the size of the individual molecule, across molecular assem...

  1. Statistical analysis of proteomics, metabolomics, and lipidomics data using mass spectrometry

    CERN Document Server

    Mertens, Bart

    2017-01-01

    This book presents an overview of computational and statistical design and analysis of mass spectrometry-based proteomics, metabolomics, and lipidomics data. This contributed volume provides an introduction to the special aspects of statistical design and analysis with mass spectrometry data for the new omic sciences. The text discusses common aspects of design and analysis between and across all (or most) forms of mass spectrometry, while also providing special examples of application with the most common forms of mass spectrometry. Also covered are applications of computational mass spectrometry not only in clinical study but also in the interpretation of omics data in plant biology studies. Omics research fields are expected to revolutionize biomolecular research by the ability to simultaneously profile many compounds within either patient blood, urine, tissue, or other biological samples. Mass spectrometry is one of the key analytical techniques used in these new omic sciences. Liquid chromatography mass ...

  2. Structural characterization of ether lipids from the archaeon Sulfolobus islandicus by high-resolution shotgun lipidomics

    DEFF Research Database (Denmark)

    Jensen, Sara Munk; Brandl, Martin; Treusch, Alexander H

    2015-01-01

    The molecular structures, biosynthetic pathways and physiological functions of membrane lipids produced by organisms in the domain Archaea are poorly characterized as compared with that of counterparts in Bacteria and Eukaryota. Here we report on the use of high-resolution shotgun lipidomics......-resolution Fourier transform mass spectrometry using an ion trap-orbitrap mass spectrometer. This analysis identified five clusters of molecular ions that matched ether lipids in the database with sub-ppm mass accuracy. To structurally characterize and validate the identities of the potential lipid species, we...... performed structural analysis using multistage activation on the ion trap-orbitrap instrument as well as tandem mass analysis using a quadrupole time-of-flight machine. Our analysis identified four ether lipid species previously reported in Archaea, and one ether lipid species that had not been described...

  3. TCW: transcriptome computational workbench.

    Science.gov (United States)

    Soderlund, Carol; Nelson, William; Willer, Mark; Gang, David R

    2013-01-01

    The analysis of transcriptome data involves many steps and various programs, along with organization of large amounts of data and results. Without a methodical approach for storage, analysis and query, the resulting ad hoc analysis can lead to human error, loss of data and results, inefficient use of time, and lack of verifiability, repeatability, and extensibility. The Transcriptome Computational Workbench (TCW) provides Java graphical interfaces for methodical analysis for both single and comparative transcriptome data without the use of a reference genome (e.g. for non-model organisms). The singleTCW interface steps the user through importing transcript sequences (e.g. Illumina) or assembling long sequences (e.g. Sanger, 454, transcripts), annotating the sequences, and performing differential expression analysis using published statistical programs in R. The data, metadata, and results are stored in a MySQL database. The multiTCW interface builds a comparison database by importing sequence and annotation from one or more single TCW databases, executes the ESTscan program to translate the sequences into proteins, and then incorporates one or more clusterings, where the clustering options are to execute the orthoMCL program, compute transitive closure, or import clusters. Both singleTCW and multiTCW allow extensive query and display of the results, where singleTCW displays the alignment of annotation hits to transcript sequences, and multiTCW displays multiple transcript alignments with MUSCLE or pairwise alignments. The query programs can be executed on the desktop for fastest analysis, or from the web for sharing the results. It is now affordable to buy a multi-processor machine, and easy to install Java and MySQL. By simply downloading the TCW, the user can interactively analyze, query and view their data. The TCW allows in-depth data mining of the results, which can lead to a better understanding of the transcriptome. TCW is freely available from www.agcol.arizona.edu/software/tcw.

  4. Lipidomic profiling of patient-specific iPSC-derived hepatocyte-like cells

    Directory of Open Access Journals (Sweden)

    Mostafa Kiamehr

    2017-09-01

    Full Text Available Hepatocyte-like cells (HLCs differentiated from human induced pluripotent stem cells (iPSCs offer an alternative model to primary human hepatocytes to study lipid aberrations. However, the detailed lipid profile of HLCs is yet unknown. In the current study, functional HLCs were differentiated from iPSCs generated from dermal fibroblasts of three individuals by a three-step protocol through the definitive endoderm (DE stage. In parallel, detailed lipidomic analyses as well as gene expression profiling of a set of lipid-metabolism-related genes were performed during the entire differentiation process from iPSCs to HLCs. Additionally, fatty acid (FA composition of the cell culture media at different stages was determined. Our results show that major alterations in the molecular species of lipids occurring during DE and early hepatic differentiation stages mainly mirror the quality and quantity of the FAs supplied in culture medium at each stage. Polyunsaturated phospholipids and sphingolipids with a very long FA were produced in the cells at a later stage of differentiation. This work uncovers the previously unknown lipid composition of iPSC-HLCs and its alterations during the differentiation in conjunction with the expression of key lipid-associated genes. Together with biochemical, functional and gene expression measurements, the lipidomic analyses allowed us to improve our understanding of the concerted influence of the exogenous metabolite supply and cellular biosynthesis essential for iPSC-HLC differentiation and function. Importantly, the study describes in detail a cell model that can be applied in exploring, for example, the lipid metabolism involved in the development of fatty liver disease or atherosclerosis.

  5. Serum metabolome and lipidome changes in adult patients with primary dengue infection.

    Directory of Open Access Journals (Sweden)

    Liang Cui

    Full Text Available Dengue virus (DENV is the most widespread arbovirus with an estimated 100 million infections occurring every year. Endemic in the tropical and subtropical areas of the world, dengue fever/dengue hemorrhagic fever (DF/DHF is emerging as a major public health concern. The complex array of concurrent host physiologic changes has hampered a complete understanding of underlying molecular mechanisms of dengue pathogenesis.Systems level characterization of serum metabolome and lipidome of adult DF patients at early febrile, defervescence, and convalescent stages of DENV infection was performed using liquid chromatography- and gas chromatography-mass spectrometry. The tractability of following metabolite and lipid changes in a relatively large sample size (n = 44 across three prominent infection stages allowed the identification of critical physiologic changes that coincided with the different stages. Sixty differential metabolites were identified in our metabolomics analysis and the main metabolite classes were free fatty acids, acylcarnitines, phospholipids, and amino acids. Major perturbed metabolic pathways included fatty acid biosynthesis and β-oxidation, phospholipid catabolism, steroid hormone pathway, etc., suggesting the multifactorial nature of human host responses. Analysis of phospholipids and sphingolipids verified the temporal trends and revealed association with lymphocytes and platelets numbers. These metabolites were significantly perturbed during the early stages, and normalized to control levels at convalescent stage, suggesting their potential utility as prognostic markers.DENV infection causes temporally distinct serum metabolome and lipidome changes, and many of the differential metabolites are involved in acute inflammatory responses. Our global analyses revealed early anti-inflammatory responses working in concert to modulate early pro-inflammatory processes, thus preventing the host from development of pathologies by excessive

  6. Opportunistic activation of TRP receptors by endogenous lipids: exploiting lipidomics to understand TRP receptor cellular communication.

    Science.gov (United States)

    Bradshaw, Heather B; Raboune, Siham; Hollis, Jennifer L

    2013-03-19

    Transient receptor potential channels (TRPs) form a large family of ubiquitous non-selective cation channels that function as cellular sensors and in many cases regulate intracellular calcium. Identification of the endogenous ligands that activate these TRP receptors is still under intense investigation with the majority of these channels still remaining "orphans." That these channels respond to a variety of external stimuli (e.g. plant-derived lipids, changes in temperature, and changes in pH) provides a framework for their abilities as cellular sensors, however, the mechanism of direct activation is still under much debate and research. In the cases where endogenous ligands (predominately lipids) have shown direct activation of a channel, multiple ligands have been shown to activate the same channel suggesting that these receptors are "promiscuous" in nature. Lipidomics of a growing class of endogenous lipids, N-acyl amides, the most famous of which is N-arachidonoyl ethanolamine (the endogenous cannabinoid, Anandamide) is providing a novel set of ligands that have been shown to activate some members of the TRP family and have the potential to deorphanize many more. Here it is argued that activation of TRPV receptors, a subset of the larger family of TRPs, by multiple endogenous lipids that are structurally analogous is a model system to drive our understanding that many TRP receptors are not promiscuous, but are more characteristically "opportunistic" in nature; exploiting the structural similarity and biosynthesis of a narrow range of analogous endogenous lipids. In addition, this manuscript will compare the activation properties of TRPC5 to the activity profile of an "orphan" lipid, N-palmitoyl glycine; further demonstrating that lipidomics aimed at expanding our knowledge of the family of N-acyl amides has the potential to provide novel avenues of research for TRP receptors. Copyright © 2012 Elsevier Inc. All rights reserved.

  7. Software ion scan functions in analysis of glycomic and lipidomic MS/MS datasets.

    Science.gov (United States)

    Haramija, Marko

    2018-03-01

    Hardware ion scan functions unique to tandem mass spectrometry (MS/MS) mode of data acquisition, such as precursor ion scan (PIS) and neutral loss scan (NLS), are important for selective extraction of key structural data from complex MS/MS spectra. However, their software counterparts, software ion scan (SIS) functions, are still not regularly available. Software ion scan functions can be easily coded for additional functionalities, such as software multiple precursor ion scan, software no ion scan, and software variable ion scan functions. These are often necessary, since they allow more efficient analysis of complex MS/MS datasets, often encountered in glycomics and lipidomics. Software ion scan functions can be easily coded by using modern script languages and can be independent of instrument manufacturer. Here we demonstrate the utility of SIS functions on a medium-size glycomic MS/MS dataset. Knowledge of sample properties, as well as of diagnostic and conditional diagnostic ions crucial for data analysis, was needed. Based on the tables constructed with the output data from the SIS functions performed, a detailed analysis of a complex MS/MS glycomic dataset could be carried out in a quick, accurate, and efficient manner. Glycomic research is progressing slowly, and with respect to the MS experiments, one of the key obstacles for moving forward is the lack of appropriate bioinformatic tools necessary for fast analysis of glycomic MS/MS datasets. Adding novel SIS functionalities to the glycomic MS/MS toolbox has a potential to significantly speed up the glycomic data analysis process. Similar tools are useful for analysis of lipidomic MS/MS datasets as well, as will be discussed briefly. Copyright © 2017 John Wiley & Sons, Ltd.

  8. Breast Milk Lipidome Is Associated with Early Growth Trajectory in Preterm Infants

    Science.gov (United States)

    Moyon, Thomas; Antignac, Jean-Philippe; Qannari, El Mostafa; Croyal, Mikaël; Soumah, Mohamed; David-Sochard, Agnès; Billard, Hélène; Legrand, Arnaud; Boscher, Cécile; Darmaun, Dominique; Rozé, Jean-Christophe

    2018-01-01

    Human milk is recommended for feeding preterm infants. The current pilot study aims to determine whether breast-milk lipidome had any impact on the early growth-pattern of preterm infants fed their own mother’s milk. A prospective-monocentric-observational birth-cohort was established, enrolling 138 preterm infants, who received their own mother’s breast-milk throughout hospital stay. All infants were ranked according to the change in weight Z-score between birth and hospital discharge. Then, we selected infants who experienced “slower” (n = 15, −1.54 ± 0.42 Z-score) or “faster” (n = 11, −0.48 ± 0.19 Z-score) growth; as expected, although groups did not differ regarding gestational age, birth weight Z-score was lower in the “faster-growth” group (0.56 ± 0.72 vs. −1.59 ± 0.96). Liquid chromatography–mass spectrometry lipidomic signatures combined with multivariate analyses made it possible to identify breast-milk lipid species that allowed clear-cut discrimination between groups. Validation of the selected biomarkers was performed using multidimensional statistical, false-discovery-rate and ROC (Receiver Operating Characteristic) tools. Breast-milk associated with faster growth contained more medium-chain saturated fatty acid and sphingomyelin, dihomo-γ-linolenic acid (DGLA)-containing phosphethanolamine, and less oleic acid-containing triglyceride and DGLA-oxylipin. The ability of such biomarkers to predict early-growth was validated in presence of confounding clinical factors but remains to be ascertained in larger cohort studies. PMID:29385065

  9. Elevated GM3 plasma concentration in idiopathic Parkinson's disease: A lipidomic analysis.

    Directory of Open Access Journals (Sweden)

    Robin B Chan

    Full Text Available Parkinson's disease (PD is a common neurodegenerative disease whose pathological hallmark is the accumulation of intracellular α-synuclein aggregates in Lewy bodies. Lipid metabolism dysregulation may play a significant role in PD pathogenesis; however, large plasma lipidomic studies in PD are lacking. In the current study, we analyzed the lipidomic profile of plasma obtained from 150 idiopathic PD patients and 100 controls, taken from the 'Spot' study at Columbia University Medical Center in New York. Our mass spectrometry based analytical panel consisted of 520 lipid species from 39 lipid subclasses including all major classes of glycerophospholipids, sphingolipids, glycerolipids and sterols. Each lipid species was analyzed using a logistic regression model. The plasma concentrations of two lipid subclasses, triglycerides and monosialodihexosylganglioside (GM3, were different between PD and control participants. GM3 ganglioside concentration had the most significant difference between PD and controls (1.531±0.037 pmol/μl versus 1.337±0.040 pmol/μl respectively; p-value = 5.96E-04; q-value = 0.048; when normalized to total lipid: p-value = 2.890E-05; q-value = 2.933E-03. Next, we used a collection of 20 GM3 and glucosylceramide (GlcCer species concentrations normalized to total lipid to perform a ROC curve analysis, and found that these lipids compare favorably with biomarkers reported in previous studies (AUC = 0.742 for males, AUC = 0.644 for females. Our results suggest that higher plasma GM3 levels are associated with PD. GM3 lies in the same glycosphingolipid metabolic pathway as GlcCer, a substrate of the enzyme glucocerebrosidase, which has been associated with PD. These findings are consistent with previous reports implicating lower glucocerebrosidase activity with PD risk.

  10. Proteomic and lipidomic signatures of lipid metabolism in NASH-associated hepatocellular carcinoma.

    Science.gov (United States)

    Muir, Kyle; Hazim, Antonious; He, Ying; Peyressatre, Marion; Kim, Do-Young; Song, Xiaoling; Beretta, Laura

    2013-08-01

    Nonalcoholic steatohepatitis (NASH) is a common preneoplastic condition of hepatocellular carcinoma (HCC). Mice with hepatocytic deletion of Pten develop NASH and HCC later in life. This model is highly valuable for studies aimed at identifying the molecular mechanism by which metabolic disorders contribute to tumor development. We applied proteomic and lipidomic profiling approaches to Pten-null NASH liver and tumors. Circulating fatty acid composition was also characterized in these mice. The relevance to human NASH and HCC was further validated. This integrative proteomic and lipidomic study from mouse to human and from liver to blood identified the following disease signatures: (i) an HCC signature: upregulated hepatic scd1/scd2, fads2, and acsl5:acsl1 ratio, elevated vaccenic and erucic acids, and reduced margaric and linoleic acids in both liver and plasma; (ii) a NASH signature that correlates with tumor burden: upregulated hepatic elovl6, elevated oleic, adrenic, and osbond acids, and reduced cervonic acid in liver and plasma; and (iii) a NASH signature: reduced hepatic and circulating lignoceric and eicosapentaenoic acids. Altogether, these results show the role of lipid-modifying enzymes converting saturated fatty acids (SFA) to monounsaturated fatty acids (MUFA) in HCC and the importance of an increased ratio of long chain n6-polyunsaturated fatty acids over n3-polyunsaturated fatty acids in NASH and HCC risk. They also highlight the relevance of the Pten-null model for studies related to NASH and HCC and show that circulating lipid metabolome provides a direct read of lipid changes in the liver. Most importantly, novel candidate targets for HCC diagnosis, therapy, risk assessment, and prevention were identified. ©2013 AACR.

  11. NMR-based lipidomic analysis of blood lipoproteins differentiates the progression of coronary heart disease.

    Science.gov (United States)

    Kostara, Christina E; Papathanasiou, Athanasios; Psychogios, Nikolaos; Cung, Manh Thong; Elisaf, Moses S; Goudevenos, John; Bairaktari, Eleni T

    2014-05-02

    Abnormal lipid composition and metabolism of plasma lipoproteins play a crucial role in the pathogenesis of coronary heart disease (CHD). A (1)H NMR-based lipidomic approach was used to investigate the correlation of coronary artery stenosis with the atherogenic (non-HDL) and atheroprotective (HDL) lipid profiles in 99 patients with CHD of various stages of disease and compared with 60 patients with normal coronary arteries (NCA), all documented in coronary angiography. The pattern recognition models created from lipid profiles predicted the presence of CHD with a sensitivity of 87% and a specificity of 88% in the HDL model and with 90% and 89% in the non-HDL model, respectively. Patients with mild, moderate, and severe coronary artery stenosis were progressively differentiated from those with NCA in the non-HDL model with a statistically significant separation of severe stage from both mild and moderate. In the HDL model, the progressive differentiation of the disease stages was statistically significant only between patients with mild and severe coronary artery stenosis. The lipid constituents of lipoproteins that mainly characterized the initial stages and then the progression of the disease were the high levels of saturated fatty acids in lipids in both HDL and non-HDL particles, the low levels of HDL-phosphatidylcholine, HDL-sphingomyelin, and omega-3 fatty acids and linoleic acid in lipids in non-HDL particles. The conventional lipid marker, total cholesterol, found in low levels in HDL and in high levels in non-HDL, also contributed to the onset of the disease but with a much lower coefficient of significance. (1)H NMR-based lipidomic analysis of atherogenic and atheroprotective lipoproteins could contribute to the early evaluation of the onset of coronary artery disease and possibly to the establishment of an appropriate therapeutic option.

  12. Quantitative lipidomic analysis of plasma and plasma lipoproteins using MALDI-TOF mass spectrometry.

    Science.gov (United States)

    Serna, Jorge; García-Seisdedos, David; Alcázar, Alberto; Lasunción, Miguel Ángel; Busto, Rebeca; Pastor, Óscar

    2015-07-01

    Knowledge of the plasma lipid composition is essential to clarify the specific roles of different lipid species in various pathophysiological processes. In this study, we developed an analytical strategy combining high-performance liquid chromatography with evaporative light scattering detection (HPLC-ELSD) and off-line coupling with matrix-assisted laser desorption/ionization with time-of-flight mass spectrometry (MALDI-TOF/MS) to determine the composition of plasma and major lipoproteins at two levels, lipid classes and lipid species. We confirmed the suitability of MALDI-TOF/MS as a quantitative measurement tool studying the linearity and repeatability for triglycerides (TG), phosphatidylethanolamine (PE) and phosphatidylcholine (PC). Moreover, data obtained with this method were correlated with other lipid classes and species measurements using currently available technologies. To establish the potential utility of our approach, human plasma very low density- (VLDL), low density- (LDL) and high density- (HDL) lipoproteins from 10 healthy donors were separated using ultracentrifugation, and compositions of nine lipid classes, cholesteryl esters (CE), TG, free cholesterol (FC), PE, phosphatidylinositol (PI), sulfatides (S), PC, lysophosphatidylcholine (LPC) and sphingomyelin (SM), analyzed. In total, 157 lipid species in plasma, 182 in LDL, 171 in HDL, and 148 in VLDL were quantified. The lipidomic profile was consistent with known differences in lipid classes, but also revealed unexpected differences in lipid species distribution of lipoproteins, particularly for LPC and SM. In summary, the methodology developed in this study constitutes a valid approach to determine the lipidomic composition of plasma and lipoproteins. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

  13. Children and Complementary Health Approaches

    Science.gov (United States)

    ... review and meta-analysis. Annals of Allergy, Asthma & Immunology . 2014;112(6):503–510. Ethical Conduct of ... Print this page Health Topics A–Z Related Topics Complementary, Alternative, or Integrative Health: What’s In a ...

  14. Ibuanyidanda (Complementary Reflection), Communalism and ...

    African Journals Online (AJOL)

    Fr. Prof. Asouzu

    Glossary of Igbo Terms and Phrases ihe ahụ na anya ... other words, it is in mutual dependence that the feeling of intimacy found among kindred ..... Complementary Reflection, Communalism and Theory Formulation in African Philosophy 25.

  15. Cancer and Complementary Health Approaches

    Science.gov (United States)

    ... According to the 2007 National Health Interview Survey (NHIS), which included a comprehensive survey on the use ... their use of complementary health approaches. In the NHIS, survey respondents who had been diagnosed with cancer ...

  16. BASED COMPLEMENTARY FOODS USING GERMINAT

    African Journals Online (AJOL)

    user

    2010-08-08

    Aug 8, 2010 ... Malnutrition affects physical growth, morbidity, mortality, cognitive development, reproduction, and ... malnutrition. Development of complementary foods is guided by nutritional value, acceptability, availability and affordability of raw materials, and simplicity of food processing ... (Memmert, Germany) at 55. 0.

  17. Comprehensive Lipidome-Wide Profiling Reveals Dynamic Changes of Tea Lipids during Manufacturing Process of Black Tea.

    Science.gov (United States)

    Li, Jia; Hua, Jinjie; Zhou, Qinghua; Dong, Chunwang; Wang, Jinjin; Deng, Yuliang; Yuan, Haibo; Jiang, Yongwen

    2017-11-22

    As important biomolecules in Camellia sinensis L., lipids undergo substantial changes during black tea manufacture, which is considered to contribute to tea sensory quality. However, limited by analytical capacity, detailed lipid composition and its dynamic changes during black tea manufacture remain unclear. Herein, we performed tea lipidome profiling using high resolution liquid chromatography coupled to mass spectrometry (LC-MS), which allows simultaneous and robust analysis of 192 individual lipid species in black tea, covering 17 (sub)classes. Furthermore, dynamic changes of tea lipids during black tea manufacture were investigated. Significant alterations of lipid pattern were revealed, involved with chlorophyll degradation, metabolic pathways of glycoglycerolipids, and other extraplastidial membrane lipids. To our knowledge, this report presented most comprehensive coverage of lipid species in black tea. This study provides a global and in-depth metabolic map of tea lipidome during black tea manufacture.

  18. LIQUID: an-open source software for identifying lipids in LC-MS/MS-based lipidomics data

    Energy Technology Data Exchange (ETDEWEB)

    Kyle, Jennifer E.; Crowell, Kevin L.; Casey, Cameron P.; Fujimoto, Grant M.; Kim, Sangtae; Dautel, Sydney E.; Smith, Richard D.; Payne, Samuel H.; Metz, Thomas O.

    2017-01-31

    We introduce an open-source software, LIQUID, for semi-automated processing and visualization of LC-MS/MS based lipidomics data. LIQUID provides users with the capability to process high throughput data and contains a customizable target library and scoring model per project needs. The graphical user interface provides visualization of multiple lines of spectral evidence for each lipid identification, allowing rapid examination of data for making confident identifications of lipid molecular species.

  19. Lipidomic Profiling of Lung Pleural Effusion Identifies Unique Metabotype for EGFR Mutants in Non-Small Cell Lung Cancer

    OpenAIRE

    Ying Swan Ho; Lian Yee Yip; Nurhidayah Basri; Vivian Su Hui Chong; Chin Chye Teo; Eddy Tan; Kah Ling Lim; Gek San Tan; Xulei Yang; Si Yong Yeo; Mariko Si Yue Koh; Anantham Devanand; Angela Takano; Eng Huat Tan; Daniel Shao Weng Tan

    2016-01-01

    Cytology and histology forms the cornerstone for the diagnosis of non-small cell lung cancer (NSCLC) but obtaining sufficient tumour cells or tissue biopsies for these tests remains a challenge. We investigate the lipidome of lung pleural effusion (PE) for unique metabolic signatures to discriminate benign versus malignant PE and EGFR versus non-EGFR malignant subgroups to identify novel diagnostic markers that is independent of tumour cell availability. Using liquid chromatography mass spect...

  20. Lipidomic profiling reveals distinct differences in plasma lipid composition in healthy, prediabetic, and type 2 diabetic individuals

    Science.gov (United States)

    Zhong, Huanzi; Fang, Chao; Fan, Yanqun; Lu, Yan; Wen, Bo; Ren, Huahui; Hou, Guixue; Yang, Fangming; Xie, Hailiang; Jie, Zhuye; Peng, Ye; Ye, Zhiqiang; Wu, Jiegen; Zi, Jin; Zhao, Guoqing; Chen, Jiayu; Bao, Xiao; Hu, Yihe; Gao, Yan; Zhang, Jun; Yang, Huanming; Wang, Jian; Madsen, Lise; Kristiansen, Karsten

    2017-01-01

    Abstract The relationship between dyslipidemia and type 2 diabetes mellitus (T2D) has been extensively reported, but the global lipid profiles, especially in the East Asia population, associated with the development of T2D remain to be characterized. Liquid chromatography coupled to tandem mass spectrometry was applied to detect the global lipidome in the fasting plasma of 293 Chinese individuals, including 114 T2D patients, 81 prediabetic subjects, and 98 individuals with normal glucose tolerance (NGT). Both qualitative and quantitative analyses revealed a gradual change in plasma lipid features with T2D patients exhibiting characteristics close to those of prediabetic individuals, whereas they differed significantly from individuals with NGT. We constructed and validated a random forest classifier with 28 lipidomic features that effectively discriminated T2D from NGT or prediabetes. Most of the selected features significantly correlated with diabetic clinical indices. Hydroxybutyrylcarnitine was positively correlated with fasting plasma glucose, 2-hour postprandial glucose, glycated hemoglobin, and insulin resistance index (HOMA-IR). Lysophosphatidylcholines such as lysophosphatidylcholine (18:0), lysophosphatidylcholine (18:1), and lysophosphatidylcholine (18:2) were all negatively correlated with HOMA-IR. The altered plasma lipidome in Chinese T2D and prediabetic subjects suggests that lipid features may play a role in the pathogenesis of T2D and that such features may provide a basis for evaluating risk and monitoring disease development. PMID:28505362

  1. Viral infection of the marine alga Emiliania huxleyi triggers lipidome remodeling and induces the production of highly saturated triacylglycerol.

    Science.gov (United States)

    Malitsky, Sergey; Ziv, Carmit; Rosenwasser, Shilo; Zheng, Shuning; Schatz, Daniella; Porat, Ziv; Ben-Dor, Shifra; Aharoni, Asaph; Vardi, Assaf

    2016-04-01

    Viruses that infect marine photosynthetic microorganisms are major ecological and evolutionary drivers of microbial food webs, estimated to turn over more than a quarter of the total photosynthetically fixed carbon. Viral infection of the bloom-forming microalga Emiliania huxleyi induces the rapid remodeling of host primary metabolism, targeted towards fatty acid metabolism. We applied a liquid chromatography-mass spectrometry (LC-MS)-based lipidomics approach combined with imaging flow cytometry and gene expression profiling to explore the impact of viral-induced metabolic reprogramming on lipid composition. Lytic viral infection led to remodeling of the cellular lipidome, by predominantly inducing the biosynthesis of highly saturated triacylglycerols (TAGs), coupled with a significant accumulation of neutral lipids within lipid droplets. Furthermore, TAGs were found to be a major component (77%) of the lipidome of isolated virions. Interestingly, viral-induced TAGs were significantly more saturated than TAGs produced under nitrogen starvation. This study highlights TAGs as major products of the viral-induced metabolic reprogramming during the host-virus interaction and indicates a selective mode of membrane recruitment during viral assembly, possibly by budding of the virus from specialized subcellular compartments. These findings provide novel insights into the role of viruses infecting microalgae in regulating metabolism and energy transfer in the marine environment and suggest their possible biotechnological application in biofuel production. © 2016 The Authors. New Phytologist © 2016 New Phytologist Trust.

  2. Fatty acid and lipidomic data in normal and tumor colon tissues of rats fed diets with and without fish oil

    Directory of Open Access Journals (Sweden)

    Zora Djuric

    2017-08-01

    Full Text Available Data is provided to show the detailed fatty acid and lipidomic composition of normal and tumor rat colon tissues. Rats were fed either a Western fat diet or a fish oil diet, and half the rats from each diet group were treated with chemical carcinogens that induce colon cancer (azoxymethane and dextran sodium sulfate. The data show total fatty acid profiles of sera and of all the colon tissues, namely normal tissue from control rats and both normal and tumor tissues from carcinogen-treated rats, as obtained by gas chromatography with mass spectral detection. Data from lipidomic analyses of a representative subset of the colon tissue samples is also shown in heat maps generated from hierarchical cluster analysis. These data display the utility lipidomic analyses to enhance the interpretation of dietary feeding studies aimed at cancer prevention and support the findings published in the companion paper (Effects of fish oil supplementation on prostaglandins in normal and tumor colon tissue: modulation by the lipogenic phenotype of colon tumors, Djuric et al., 2017 [1].

  3. Lipidomic Profiling of Lung Pleural Effusion Identifies Unique Metabotype for EGFR Mutants in Non-Small Cell Lung Cancer.

    Science.gov (United States)

    Ho, Ying Swan; Yip, Lian Yee; Basri, Nurhidayah; Chong, Vivian Su Hui; Teo, Chin Chye; Tan, Eddy; Lim, Kah Ling; Tan, Gek San; Yang, Xulei; Yeo, Si Yong; Koh, Mariko Si Yue; Devanand, Anantham; Takano, Angela; Tan, Eng Huat; Tan, Daniel Shao Weng; Lim, Tony Kiat Hon

    2016-10-14

    Cytology and histology forms the cornerstone for the diagnosis of non-small cell lung cancer (NSCLC) but obtaining sufficient tumour cells or tissue biopsies for these tests remains a challenge. We investigate the lipidome of lung pleural effusion (PE) for unique metabolic signatures to discriminate benign versus malignant PE and EGFR versus non-EGFR malignant subgroups to identify novel diagnostic markers that is independent of tumour cell availability. Using liquid chromatography mass spectrometry, we profiled the lipidomes of the PE of 30 benign and 41 malignant cases with or without EGFR mutation. Unsupervised principal component analysis revealed distinctive differences between the lipidomes of benign and malignant PE as well as between EGFR mutants and non-EGFR mutants. Docosapentaenoic acid and Docosahexaenoic acid gave superior sensitivity and specificity for detecting NSCLC when used singly. Additionally, several 20- and 22- carbon polyunsaturated fatty acids and phospholipid species were significantly elevated in the EGFR mutants compared to non-EGFR mutants. A 7-lipid panel showed great promise in the stratification of EGFR from non-EGFR malignant PE. Our data revealed novel lipid candidate markers in the non-cellular fraction of PE that holds potential to aid the diagnosis of benign, EGFR mutation positive and negative NSCLC.

  4. Lipidomic Adaptations in White and Brown Adipose Tissue in Response to Exercise Demonstrate Molecular Species-Specific Remodeling

    Directory of Open Access Journals (Sweden)

    Francis J. May

    2017-02-01

    Full Text Available Exercise improves whole-body metabolic health through adaptations to various tissues, including adipose tissue, but the effects of exercise training on the lipidome of white adipose tissue (WAT and brown adipose tissue (BAT are unknown. Here, we utilize MS/MSALL shotgun lipidomics to determine the molecular signatures of exercise-induced adaptations to subcutaneous WAT (scWAT and BAT. Three weeks of exercise training decrease specific molecular species of phosphatidic acid (PA, phosphatidylcholines (PC, phosphatidylethanolamines (PE, and phosphatidylserines (PS in scWAT and increase specific molecular species of PC and PE in BAT. Exercise also decreases most triacylglycerols (TAGs in scWAT and BAT. In summary, exercise-induced changes to the scWAT and BAT lipidome are highly specific to certain molecular lipid species, indicating that changes in tissue lipid content reflect selective remodeling in scWAT and BAT of both phospholipids and glycerol lipids in response to exercise training, thus providing a comprehensive resource for future studies of lipid metabolism pathways.

  5. TCW: transcriptome computational workbench.

    Directory of Open Access Journals (Sweden)

    Carol Soderlund

    Full Text Available BACKGROUND: The analysis of transcriptome data involves many steps and various programs, along with organization of large amounts of data and results. Without a methodical approach for storage, analysis and query, the resulting ad hoc analysis can lead to human error, loss of data and results, inefficient use of time, and lack of verifiability, repeatability, and extensibility. METHODOLOGY: The Transcriptome Computational Workbench (TCW provides Java graphical interfaces for methodical analysis for both single and comparative transcriptome data without the use of a reference genome (e.g. for non-model organisms. The singleTCW interface steps the user through importing transcript sequences (e.g. Illumina or assembling long sequences (e.g. Sanger, 454, transcripts, annotating the sequences, and performing differential expression analysis using published statistical programs in R. The data, metadata, and results are stored in a MySQL database. The multiTCW interface builds a comparison database by importing sequence and annotation from one or more single TCW databases, executes the ESTscan program to translate the sequences into proteins, and then incorporates one or more clusterings, where the clustering options are to execute the orthoMCL program, compute transitive closure, or import clusters. Both singleTCW and multiTCW allow extensive query and display of the results, where singleTCW displays the alignment of annotation hits to transcript sequences, and multiTCW displays multiple transcript alignments with MUSCLE or pairwise alignments. The query programs can be executed on the desktop for fastest analysis, or from the web for sharing the results. CONCLUSION: It is now affordable to buy a multi-processor machine, and easy to install Java and MySQL. By simply downloading the TCW, the user can interactively analyze, query and view their data. The TCW allows in-depth data mining of the results, which can lead to a better understanding of the

  6. Prototype semantic infrastructure for automated small molecule classification and annotation in lipidomics.

    Science.gov (United States)

    Chepelev, Leonid L; Riazanov, Alexandre; Kouznetsov, Alexandre; Low, Hong Sang; Dumontier, Michel; Baker, Christopher J O

    2011-07-26

    high-throughput lipidomics. Our prototype framework is capable of accurate automated classification of lipids and facile integration of lipid class information with additional data obtained with SADI web services. The potential of programming-free integration of external web services through the SADI framework offers an opportunity for development of powerful novel applications in lipidomics. We conclude that semantic web technologies can provide an accurate and versatile means of classification and annotation of lipids.

  7. Prototype semantic infrastructure for automated small molecule classification and annotation in lipidomics

    Directory of Open Access Journals (Sweden)

    Dumontier Michel

    2011-07-01

    our integrative methodology in the context of high-throughput lipidomics. Conclusions Our prototype framework is capable of accurate automated classification of lipids and facile integration of lipid class information with additional data obtained with SADI web services. The potential of programming-free integration of external web services through the SADI framework offers an opportunity for development of powerful novel applications in lipidomics. We conclude that semantic web technologies can provide an accurate and versatile means of classification and annotation of lipids.

  8. Complementary Colours for a Physicist

    Science.gov (United States)

    Babic, Vitomir; Cepic, Mojca

    2009-01-01

    This paper reports on a simple experiment which enables splitting incident light into two different modes, each having a colour exactly complementary to the other. A brief historical development of colour theories and differences in a physicist's point of view with respect to an artist's one is discussed. An experimental system for producing…

  9. Parental concerns about complementary feeding

    DEFF Research Database (Denmark)

    Nielsen, Annemette; Michaelsen, Kim F.; Holm, Lotte

    2013-01-01

    Background/objectives:To investigate and analyze differences in parental concerns during earlier and later phases of complementary feeding.Subject/methods:Eight focus group interviews were conducted with 45 mothers of children aged 7 or 13 months. Deductive and inductive coding procedures were ap......:10.1038/ejcn.2013.165....

  10. Emerging issues in complementary feeding

    DEFF Research Database (Denmark)

    Michaelsen, Kim F.; Grummer-Strawn, Laurence; Bégin, France

    2017-01-01

    the complementary feeding period is summarized. The increased availability of sugar-containing beverages and unhealthy snack foods and its negative effect on young child's diet is described. Negative effects of nonresponsive feeding and force feeding are also discussed, although few scientific studies have...

  11. Complementary therapies in social psychiatry

    DEFF Research Database (Denmark)

    Lunde, Anita; Dürr, Dorte Wiwe

    three residential homes (n= 51 / 91 respondents - response rate 56 %) shows that the most common used complementary therapy is music therapy 43%, and only 10% of residents do not use these therapies at all. Overall, 43% of residents strongly agree, that these therapies strengthens their recovery process...

  12. Industrial Evolution Through Complementary Convergence

    DEFF Research Database (Denmark)

    Frøslev Christensen, Jens

    2011-01-01

    The article addresses the dynamics through which product markets become derailed from early product life cycle (PLC)-tracks and engaged in complementary convergence with other product markets or industries. We compare and contrast the theories that can explain, respectively, the PLC...

  13. Mass Spectrometry Strategies for Clinical Metabolomics and Lipidomics in Psychiatry, Neurology, and Neuro-Oncology

    Science.gov (United States)

    Wood, Paul L

    2014-01-01

    Metabolomics research has the potential to provide biomarkers for the detection of disease, for subtyping complex disease populations, for monitoring disease progression and therapy, and for defining new molecular targets for therapeutic intervention. These potentials are far from being realized because of a number of technical, conceptual, financial, and bioinformatics issues. Mass spectrometry provides analytical platforms that address the technical barriers to success in metabolomics research; however, the limited commercial availability of analytical and stable isotope standards has created a bottleneck for the absolute quantitation of a number of metabolites. Conceptual and financial factors contribute to the generation of statistically under-powered clinical studies, whereas bioinformatics issues result in the publication of a large number of unidentified metabolites. The path forward in this field involves targeted metabolomics analyses of large control and patient populations to define both the normal range of a defined metabolite and the potential heterogeneity (eg, bimodal) in complex patient populations. This approach requires that metabolomics research groups, in addition to developing a number of analytical platforms, build sufficient chemistry resources to supply the analytical standards required for absolute metabolite quantitation. Examples of metabolomics evaluations of sulfur amino-acid metabolism in psychiatry, neurology, and neuro-oncology and of lipidomics in neurology will be reviewed. PMID:23842599

  14. Mass spectrometry strategies for clinical metabolomics and lipidomics in psychiatry, neurology, and neuro-oncology.

    Science.gov (United States)

    Wood, Paul L

    2014-01-01

    Metabolomics research has the potential to provide biomarkers for the detection of disease, for subtyping complex disease populations, for monitoring disease progression and therapy, and for defining new molecular targets for therapeutic intervention. These potentials are far from being realized because of a number of technical, conceptual, financial, and bioinformatics issues. Mass spectrometry provides analytical platforms that address the technical barriers to success in metabolomics research; however, the limited commercial availability of analytical and stable isotope standards has created a bottleneck for the absolute quantitation of a number of metabolites. Conceptual and financial factors contribute to the generation of statistically under-powered clinical studies, whereas bioinformatics issues result in the publication of a large number of unidentified metabolites. The path forward in this field involves targeted metabolomics analyses of large control and patient populations to define both the normal range of a defined metabolite and the potential heterogeneity (eg, bimodal) in complex patient populations. This approach requires that metabolomics research groups, in addition to developing a number of analytical platforms, build sufficient chemistry resources to supply the analytical standards required for absolute metabolite quantitation. Examples of metabolomics evaluations of sulfur amino-acid metabolism in psychiatry, neurology, and neuro-oncology and of lipidomics in neurology will be reviewed.

  15. Targeted Lipidomics in Drosophila melanogaster Identifies Novel 2-Monoacylglycerols and N-acyl Amides

    Science.gov (United States)

    Takacs, Sara M.; Stuart, Jordyn M.; Basnet, Arjun; Raboune, Siham; Widlanski, Theodore S.; Doherty, Patrick; Bradshaw, Heather B.

    2013-01-01

    Lipid metabolism is critical to coordinate organ development and physiology in response to tissue-autonomous signals and environmental cues. Changes to the availability and signaling of lipid mediators can limit competitiveness, adaptation to environmental stressors, and augment pathological processes. Two classes of lipids, the N-acyl amides and the 2-acyl glycerols, have emerged as important signaling molecules in a wide range of species with important signaling properties, though most of what is known about their cellular functions is from mammalian models. Therefore, expanding available knowledge on the repertoire of these lipids in invertebrates will provide additional avenues of research aimed at elucidating biosynthetic, metabolic, and signaling properties of these molecules. Drosophila melanogaster is a commonly used organism to study intercellular communication, including the functions of bioactive lipids. However, limited information is available on the molecular identity of lipids with putative biological activities in Drosophila. Here, we used a targeted lipidomics approach to identify putative signaling lipids in third instar Drosophila larvae, possessing particularly large lipid mass in their fat body. We identified 2-linoleoyl glycerol, 2-oleoyl glycerol, and 45 N-acyl amides in larval tissues, and validated our findings by the comparative analysis of Oregon-RS, Canton-S and w1118 strains. Data here suggest that Drosophila represent another model system to use for the study of 2-acyl glycerol and N-acyl amide signaling. PMID:23874457

  16. Neuroprotection of dietary virgin olive oil on brain lipidomics during stroke.

    Science.gov (United States)

    Rabiei, Zahra; Bigdeli, Mohammad Reza; Rasoulian, Bahram

    2013-08-01

    Recent studies suggest that dietary virgin olive oil reduces hypoxia-reoxygenation injury in rat brain. This study investigated the effect of pretreatment with different doses of dietary virgin olive oil on brain lipidomics during stroke. In this experimental trial, 60 male Wistar rats were studied in 5 groups of 12 each. The control group received distilled water while three treatment groups received oral virgin olive oil for 30 days (0.25, 0.5 and 0.75 ml/kg/day respectively). Also the sham group received distilled water. Two hours after the last dose, the animals divided two groups. The middle cerebral artery occlusion (MCAO) group subjected to 60 min of middle cerebral artery occlusion (MCAO) and intact groups for brain lipids analysis. The brain phosphatidylcholine, cholesterol ester and cholesterol levels increased significantly in doses of 0.5 and 0.75 ml/kg/day compare with control group. VOO in all three doses increased the brain triglyceride levels. VOO with dose 0.75 ml/kg increased the brain cerebroside levels when compared with control group. VOO pretreatment for 30 days decreased the brain ceramide levels in doses of 0.5 and 0.75 ml/kg/day (p<0.05). Although further studies are needed, the results indicate that the VOO pretreatment improved the injury of ischemia and reperfusion and might be beneficial in patients with these disorders and seems to partly exert their effects via change in brain lipid levels in rat.

  17. Establishing Substantial Equivalence: Transcriptomics

    Science.gov (United States)

    Baudo, María Marcela; Powers, Stephen J.; Mitchell, Rowan A. C.; Shewry, Peter R.

    Regulatory authorities in Western Europe require transgenic crops to be substantially equivalent to conventionally bred forms if they are to be approved for commercial production. One way to establish substantial equivalence is to compare the transcript profiles of developing grain and other tissues of transgenic and conventionally bred lines, in order to identify any unintended effects of the transformation process. We present detailed protocols for transcriptomic comparisons of developing wheat grain and leaf material, and illustrate their use by reference to our own studies of lines transformed to express additional gluten protein genes controlled by their own endosperm-specific promoters. The results show that the transgenes present in these lines (which included those encoding marker genes) did not have any significant unpredicted effects on the expression of endogenous genes and that the transgenic plants were therefore substantially equivalent to the corresponding parental lines.

  18. Developmental transcriptome of Aplysia californica'

    KAUST Repository

    Heyland, Andreas; Vue, Zer; Voolstra, Christian R.; Medina, Mó nica; Moroz, Leonid L.

    2010-01-01

    developmental transcriptome with similar studies in the zebra fish Danio rerio, the fruit fly Drosophila melanogaster, the nematode Caenorhabditis elegans, and other studies on molluscs suggests an overall highly divergent pattern of gene regulatory mechanisms

  19. Integrated transcriptomic and proteomic evaluation of gentamicin nephrotoxicity in rats

    International Nuclear Information System (INIS)

    Com, Emmanuelle; Boitier, Eric; Marchandeau, Jean-Pierre; Brandenburg, Arnd; Schroeder, Susanne; Hoffmann, Dana; Mally, Angela; Gautier, Jean-Charles

    2012-01-01

    Gentamicin is an aminoglycoside antibiotic, which induces renal tubular necrosis in rats. In the context of the European InnoMed PredTox project, transcriptomic and proteomic studies were performed to provide new insights into the molecular mechanisms of gentamicin-induced nephrotoxicity. Male Wistar rats were treated with 25 and 75 mg/kg/day subcutaneously for 1, 3 and 14 days. Histopathology observations showed mild tubular degeneration/necrosis and regeneration and moderate mononuclear cell infiltrate after long-term treatment. Transcriptomic data indicated a strong treatment-related gene expression modulation in kidney and blood cells at the high dose after 14 days of treatment, with the regulation of 463 and 3241 genes, respectively. Of note, the induction of NF-kappa B pathway via the p38 MAPK cascade in the kidney, together with the activation of T-cell receptor signaling in blood cells were suggestive of inflammatory processes in relation with the recruitment of mononuclear cells in the kidney. Proteomic results showed a regulation of 163 proteins in kidney at the high dose after 14 days of treatment. These protein modulations were suggestive of a mitochondrial dysfunction with impairment of cellular energy production, induction of oxidative stress, an effect on protein biosynthesis and on cellular assembly and organization. Proteomic results also provided clues for potential nephrotoxicity biomarkers such as AGAT and PRBP4 which were strongly modulated in the kidney. Transcriptomic and proteomic data turned out to be complementary and their integration gave a more comprehensive insight into the putative mode of nephrotoxicity of gentamicin which was in accordance with histopathological findings. -- Highlights: ► Gentamicin induces renal tubular necrosis in rats. ► The mechanisms of gentamicin nephrotoxicity remain still elusive. ► Transcriptomic and proteomic analyses were performed to study this toxicity in rats. ► Transcriptomic and proteomic

  20. Phenotypic malignant changes and untargeted lipidomic analysis of long-term exposed prostate cancer cells to endocrine disruptors

    International Nuclear Information System (INIS)

    Bedia, Carmen; Dalmau, Núria; Jaumot, Joaquim; Tauler, Romà

    2015-01-01

    Endocrine disruptors (EDs) are a class of environmental toxic molecules able to interfere with the normal hormone metabolism. Numerous studies involve EDs exposure to initiation and development of cancers, including prostate cancer. In this work, three different EDs (aldrin, aroclor 1254 and chlorpyrifos (CPF)) were investigated as potential inducers of a malignant phenotype in DU145 prostate cancer cells after a chronic exposure. Epithelial to mesenchymal transition (EMT) induction, proliferation, migration, colony formation and release of metalloproteinase 2 (MMP-2) were analyzed in 50-day exposed cells to the selected EDs. As a result, aldrin and CPF exposure led to an EMT induction (loss of 16% and 14% of E-cadherin levels, respectively, compared to the unexposed cells). Aroclor and CPF presented an increased migration (134% and 126%, respectively), colony formation (204% and 144%, respectively) and MMP-2 release (137% in both cases) compared to the unexposed cells. An untargeted lipidomic analysis was performed to decipher the lipids involved in the observed transformations. As general results, aldrin exposure showed a global decrease in phospholipids and sphingolipids, and aroclor and CPF showed an increase of certain phospholipids, glycosphingolipids as well as a remarkable increase of some cardiolipin species. Furthermore, the three exposures resulted in an increase of some triglyceride species. In conclusion, some significant changes in lipids were identified and thus we postulate that some lipid compounds and lipid metabolic pathways could be involved in the acquisition of the malignant phenotype in exposed prostate cancer cells to the selected EDs. - Highlights: • Aldrin, aroclor and chlorpyrifos induced an aggressive phenotype in DU145 cells. • An untargeted lipidomic analysis has been performed on chronic exposed cells. • Lipidomic results showed changes in specific lipid species under chronic exposure. • These lipids may have a role in the

  1. Phenotypic malignant changes and untargeted lipidomic analysis of long-term exposed prostate cancer cells to endocrine disruptors

    Energy Technology Data Exchange (ETDEWEB)

    Bedia, Carmen, E-mail: carmen.bedia@idaea.csic.es; Dalmau, Núria, E-mail: nuria.dalmau@idaea.csic.es; Jaumot, Joaquim, E-mail: joaquim.jaumot@idaea.csic.es; Tauler, Romà, E-mail: roma.tauler@idaea.csic.es

    2015-07-15

    Endocrine disruptors (EDs) are a class of environmental toxic molecules able to interfere with the normal hormone metabolism. Numerous studies involve EDs exposure to initiation and development of cancers, including prostate cancer. In this work, three different EDs (aldrin, aroclor 1254 and chlorpyrifos (CPF)) were investigated as potential inducers of a malignant phenotype in DU145 prostate cancer cells after a chronic exposure. Epithelial to mesenchymal transition (EMT) induction, proliferation, migration, colony formation and release of metalloproteinase 2 (MMP-2) were analyzed in 50-day exposed cells to the selected EDs. As a result, aldrin and CPF exposure led to an EMT induction (loss of 16% and 14% of E-cadherin levels, respectively, compared to the unexposed cells). Aroclor and CPF presented an increased migration (134% and 126%, respectively), colony formation (204% and 144%, respectively) and MMP-2 release (137% in both cases) compared to the unexposed cells. An untargeted lipidomic analysis was performed to decipher the lipids involved in the observed transformations. As general results, aldrin exposure showed a global decrease in phospholipids and sphingolipids, and aroclor and CPF showed an increase of certain phospholipids, glycosphingolipids as well as a remarkable increase of some cardiolipin species. Furthermore, the three exposures resulted in an increase of some triglyceride species. In conclusion, some significant changes in lipids were identified and thus we postulate that some lipid compounds and lipid metabolic pathways could be involved in the acquisition of the malignant phenotype in exposed prostate cancer cells to the selected EDs. - Highlights: • Aldrin, aroclor and chlorpyrifos induced an aggressive phenotype in DU145 cells. • An untargeted lipidomic analysis has been performed on chronic exposed cells. • Lipidomic results showed changes in specific lipid species under chronic exposure. • These lipids may have a role in the

  2. Integrative Medicine and Complementary and Alternative Therapies

    Science.gov (United States)

    ... complementary therapies with your healthcare team: Are there complementary therapies that you would recommend? What research is available about this therapy’s safety and effectiveness? What are the benefits and risks of this ...

  3. Office of Cancer Complementary and Alternative Medicine

    Science.gov (United States)

    ... C Research. Information. Outreach. The Office of Cancer Complementary and Alternative Medicine (OCCAM) was established in October 1998 to coordinate ... National Cancer Institute (NCI) in the arena of complementary and alternative medicine (CAM). More about us. CAM at the NCI ...

  4. African Journal of Traditional, Complementary and Alternative ...

    African Journals Online (AJOL)

    African Journal of Traditional, Complementary and Alternative Medicines: Advanced Search. Journal Home > African Journal of Traditional, Complementary and Alternative Medicines: Advanced Search. Log in or Register to get access to full text downloads.

  5. Non-targeted metabolomics and lipidomics LC-MS data from maternal plasma of 180 healthy pregnant women

    DEFF Research Database (Denmark)

    Luan, Hemi; Meng, Nan; Liu, Ping

    2015-01-01

    Background: Metabolomics has the potential to be a powerful and sensitive approach for investigating the low molecular weight metabolite profiles present in maternal fluids and their role in pregnancy.Findings: In this Data Note, LC-MS metabolome, lipidome and carnitine profiling data were...... collected from 180 healthy pregnant women, representing six time points spanning all three trimesters, and providing sufficient coverage to model the progression of normal pregnancy.Conclusions: As a relatively large scale, real-world dataset with robust numbers of quality control samples, the data...

  6. Plasma and serum lipidomics of healthy white adults shows characteristic profiles by subjects' gender and age.

    Directory of Open Access Journals (Sweden)

    Masaki Ishikawa

    Full Text Available Blood is a commonly used biofluid for biomarker discovery. Although blood lipid metabolites are considered to be potential biomarker candidates, their fundamental properties are not well characterized. We aimed to (1 investigate the matrix type (serum vs. plasma that may be preferable for lipid biomarker exploration, (2 elucidate age- and gender-associated differences in lipid metabolite levels, and (3 examine the stability of lipid metabolites in matrix samples subjected to repeated freeze-thaw cycles. Using liquid chromatography-mass spectrometry, we performed lipidomic analyses for fasting plasma and serum samples for four groups (15 subjects/group of young and elderly (25-34 and 55-64 years old, respectively males and females and for an additional aliquot of samples from young males, which were subjected to repeated freeze-thaw cycles. Lysophosphatidylcholine and diacylglycerol levels were higher in serum than in plasma samples, suggesting that the clotting process influences serum lipid metabolite levels. Gender-associated differences highlighted that the levels of many sphingomyelin species were significantly higher in females than in males, irrespective of age and matrix (plasma and serum. Age-associated differences were more prominent in females than in males, and in both matrices, levels of many triacylglycerols were significantly higher in elderly females than in young females. Plasma and serum levels of most lipid metabolites were reduced by freeze-thawing. Our results indicate that plasma is an optimal matrix for exploring lipid biomarkers because it represents the original properties of an individual's blood sample. In addition, the levels of some blood lipid species of healthy adults showed gender- and age-associated differences; thus, this should be considered during biomarker exploration and its application in diagnostics. Our fundamental findings on sample selection and handling procedures for measuring blood lipid metabolites

  7. Lipidomic profiling of di- and tri-acylglycerol species in weight-controlled mice.

    Directory of Open Access Journals (Sweden)

    Brenee S King

    Full Text Available Weight control by dietary calorie restriction (DCR or exercise has been shown to prevent cancer in various models. However, the mechanisms as to how weight control is beneficial are not well understood. While previous reports have investigated the effects of weight control on total lipid levels or lipid composition within cellular membranes, there has been little work surrounding changes to individual lipids following weight control interventions. In this study, using a model of skin carcinogenesis centered on the tumor promotion stage, CD-1 mice were randomly assigned into 4 groups: ad libitum and sedentary (control, ad libitum with exercise (AL+Exe, exercise with pair feeding of a diet isocaloric with control (PF+Exe, and sedentary with 20% DCR compared to control. After ten weeks, body weight and body fat percentages significantly decreased in the PF+Exe and DCR groups but not AL+Exe when compared with sedentary controls. Murine skin and plasma samples were obtained for analysis. Lipidomics using electrospray ionization MS/MS was employed to profile triacylglycerol (TG and diacylglycerol (DG species. Both plasma and tissue TG species containing fatty acid chains with length 18:1 were significantly decreased following DCR when compared to sedentary control animals. In regards to DG, the most significant changes occurred in the plasma. DG species containing fatty acids with lengths 16:1 or 18:1 were significantly decreased in PF+Exe and DCR groups when compared to sedentary controls. Due to the significant role of TG in energy storage and DG in cellular signaling, our findings of the effects of weight control on individual TG and DG species in plasma and skin tissue following exposure to a tumor promoter, may provide insight into the mechanism of weight control on cancer prevention.

  8. Lipidomics Reveals Associations of Phospholipids With Obesity and Insulin Resistance in Young Adults.

    Science.gov (United States)

    Rauschert, Sebastian; Uhl, Olaf; Koletzko, Berthold; Kirchberg, Franca; Mori, Trevor A; Huang, Rae-Chi; Beilin, Lawrence J; Hellmuth, Christian; Oddy, Wendy H

    2016-03-01

    Obesity and related diseases have become a global public health burden. Identifying biomarkers will lead to a better understanding of the underlying mechanisms associated with obesity and the pathways leading to insulin resistance (IR) and diabetes. This study aimed to identify the lipidomic biomarkers associated with obesity and IR using plasma samples from a population-based cohort of young adults. The Western Australian Pregnancy Cohort (Raine) study enrolled 2900 pregnant women from 1989 to 1991. The 20-year follow-up was conducted between March 2010 and April 2012. Participants and Samples: Plasma samples from 1176 subjects aged 20 years were analyzed using mass spectrometry-based metabolomics. Associations of analytes with markers of obesity and IR including body mass index, waist circumference, homeostasis model assessment (HOMA-IR), and insulin were examined. Analyses were stratified by body mass index and adjusted for lifestyle and other factors. Waist circumference was positively associated with seven sphingomyelins and five diacylphosphatidylcholines and negatively associated with two lysophosphatidylcholines. HOMA-IR was negatively associated with two diacylphosphatidylcholines and positively with one lysophosphatidylcholine and one diacylphosphatidylcholine. No significant association was found in the obese/overweight group of the HOMA-IR model. In the normal-weight group, one lysophosphatidylcholine was increased. A possible discriminative effect of sphingomyelins, particularly those with two double bonds, and lysophosphatidylcholines was identified between subjects with normal weight and obesity independent of low-density lipoprotein cholesterol and high-density lipoprotein cholesterol concentrations. Our results suggest weight status-dependent mechanisms for the development of IR with lysophosphatidylcholine C14:0 as a key metabolite in nonobese IR.

  9. LipidPioneer : A Comprehensive User-Generated Exact Mass Template for Lipidomics

    Science.gov (United States)

    Ulmer, Candice Z.; Koelmel, Jeremy P.; Ragland, Jared M.; Garrett, Timothy J.; Bowden, John A.

    2017-03-01

    Lipidomics, the comprehensive measurement of lipid species in a biological system, has promising potential in biomarker discovery and disease etiology elucidation. Advances in chromatographic separation, mass spectrometric techniques, and novel substrate applications continue to expand the number of lipid species observed. The total number and type of lipid species detected in a given sample are generally indicative of the sample matrix examined (e.g., serum, plasma, cells, bacteria, tissue, etc.). Current exact mass lipid libraries are static and represent the most commonly analyzed matrices. It is common practice for users to manually curate their own lists of lipid species and adduct masses; however, this process is time-consuming. LipidPioneer, an interactive template, can be used to generate exact masses and molecular formulas of lipid species that may be encountered in the mass spectrometric analysis of lipid profiles. Over 60 lipid classes are present in the LipidPioneer template and include several unique lipid species, such as ether-linked lipids and lipid oxidation products. In the template, users can add any fatty acyl constituents without limitation in the number of carbons or degrees of unsaturation. LipidPioneer accepts naming using the lipid class level (sum composition) and the LIPID MAPS notation for fatty acyl structure level. In addition to lipid identification, user-generated lipid m/z values can be used to develop inclusion lists for targeted fragmentation experiments. Resulting lipid names and m/z values can be imported into software such as MZmine or Compound Discoverer to automate exact mass searching and isotopic pattern matching across experimental data.

  10. Transcriptome States Reflect Imaging of Aging States.

    Science.gov (United States)

    Eckley, D Mark; Coletta, Christopher E; Orlov, Nikita V; Wilson, Mark A; Iser, Wendy; Bastian, Paul; Lehrmann, Elin; Zhang, Yonqing; Becker, Kevin G; Goldberg, Ilya G

    2018-06-14

    In this study, we describe a morphological biomarker that detects multiple discrete subpopulations (or "age-states") at several chronological ages in a population of nematodes (Caenorhabditis elegans). We determined the frequencies of three healthy adult states and the timing of the transitions between them across the lifespan. We used short-lived and long-lived strains to confirm the general applicability of the state classifier and to monitor state progression. This exploration revealed healthy and unhealthy states, the former being favored in long-lived strains and the latter showing delayed onset. Short-lived strains rapidly transitioned through the putative healthy state. We previously found that age-matched animals in different age-states have distinct transcriptome profiles. We isolated animals at the beginning and end of each identified state and performed microarray analysis (principal component analysis, relative sample to sample distance measurements, and gene set enrichment analysis). In some comparisons, chronologically identical individuals were farther apart than morphologically identical individuals isolated on different days. The age-state biomarker allowed assessment of aging in a novel manner, complementary to chronological age progression. We found hsp70 and some small heat shock protein genes are expressed later in adulthood, consistent with the proteostasis collapse model.

  11. Thyroid Disease and Complementary and Alternative Medicine (CAM)

    Science.gov (United States)

    ... Alternative Medicine in Thyroid Disease Complementary and Alternative Medicine in Thyroid Disease (CAM) WHAT IS COMPLEMENTARY AND ALTERNATIVE MEDICINE (CAM)? Complementary and Alternative Medicine (CAM) is defined ...

  12. Widely-targeted quantitative lipidomics methodology by supercritical fluid chromatography coupled with fast-scanning triple quadrupole mass spectrometry.

    Science.gov (United States)

    Takeda, Hiroaki; Izumi, Yoshihiro; Takahashi, Masatomo; Paxton, Thanai; Tamura, Shohei; Koike, Tomonari; Yu, Ying; Kato, Noriko; Nagase, Katsutoshi; Shiomi, Masashi; Bamba, Takeshi

    2018-05-03

    Lipidomics, the mass spectrometry-based comprehensive analysis of lipids, has attracted attention as an analytical approach to provide novel insight into lipid metabolism and to search for biomarkers. However, an ideal method for both comprehensive and quantitative analysis of lipids has not been fully developed. Herein, we have proposed a practical methodology for widely-targeted quantitative lipidome analysis using supercritical fluid chromatography fast-scanning triple-quadrupole mass spectrometry (SFC/QqQMS) and theoretically calculated a comprehensive lipid multiple reaction monitoring (MRM) library. Lipid classes can be separated by SFC with a normal phase diethylamine-bonded silica column with high-resolution, high-throughput, and good repeatability. Structural isomers of phospholipids can be monitored by mass spectrometric separation with fatty acyl-based MRM transitions. SFC/QqQMS analysis with an internal standard-dilution method offers quantitative information for both lipid class and individual lipid molecular species in the same lipid class. Additionally, data acquired using this method has advantages including reduction of misidentification and acceleration of data analysis. Using the SFC/QqQMS system, alteration of plasma lipid levels in myocardial infarction-prone rabbits to the supplementation of eicosapentaenoic acid was first observed. Our developed SFC/QqQMS method represents a potentially useful tool for in-depth studies focused on complex lipid metabolism and biomarker discovery. Published under license by The American Society for Biochemistry and Molecular Biology, Inc.

  13. Serum Oxidative Stress Markers and Lipidomic Profile to Detect NASH Patients Responsive to an Antioxidant Treatment: A Pilot Study

    Directory of Open Access Journals (Sweden)

    Paola Stiuso

    2014-01-01

    Full Text Available Liver steatosis can evolve to steatohepatitis (NASH through a series of biochemical steps related to oxidative stress in hepatocytes. Antioxidants, such as silybin, have been proposed as a treatment of patients with nonalcoholic fatty liver disease (NAFLD and NASH. In this study, we evaluated, in patients with histologically documented NASH, the oxidant/antioxidant status and lipid “fingerprint” in the serum of NASH patients, both in basal conditions and after 12 months of treatment with silybin-based food integrator Realsil (RA. The oxidant/antioxidant status analysis showed the presence of a group of patients with higher basal severity of disease (NAS scores 4.67 ± 2.5 and a second group corresponding to borderline NASH (NAS scores = 3.8 ± 1.5. The chronic treatment with RA changed the NAS score in both groups that reached the statistical significance only in group 2, in which there was also a significant decrease of serum lipid peroxidation. The lipidomic profile showed a lipid composition similar to that of healthy subjects with a restoration of the values of free cholesterol, lysoPC, SM, and PC only in group 2 of patients after treatment with RA. Conclusion. These data suggest that lipidomic and/or oxidative status of serum from patients with NASH could be useful as prognostic markers of response to an antioxidant treatment.

  14. Lipidomic data on lipid droplet triglyceride remodelling associated with protection of breast cancer cells from lipotoxic stress

    Directory of Open Access Journals (Sweden)

    Eva Jarc

    2018-06-01

    Full Text Available The data presented here is related to the research article entitled “Lipid droplets induced by secreted phospholipase A2 and unsaturated fatty acids protect breast cancer cells from nutrient and lipotoxic stress” by E. Jarc et al., Biochim. Biophys. Acta 1863 (2018 247–265. Elevated uptake of unsaturated fatty acids and lipid droplet accumulation are characteristic of aggressive cancer cells and have been associated with the cellular stress response. The present study provides lipidomic data on the triacylglycerol (TAG and phosphatidylcholine (PC composition of MDA-MB-231 breast cancer cells exposed to docosahexaenoic acid (DHA; 22:6, ω-3. Datasets provide information on the changes in lipid composition induced by depletion of adipose triglyceride lipase (ATGL and by exogenous addition of secreted phospholipase A2 (sPLA2 in DHA-treated cells. The presented alterations in lipid composition, mediated by targeting lipid droplet biogenesis and lipolysis, are associated with protection from lipotoxicity and allow further investigation into the role of lipid droplets in the resistance of cancer cells to lipotoxic stress. Keywords: Lipid droplets, Lipidomics, Adipose triglyceride lipase, Polyunsaturated fatty acid, Cancer, Phospholipase A2

  15. Online Wavelet Complementary velocity Estimator.

    Science.gov (United States)

    Righettini, Paolo; Strada, Roberto; KhademOlama, Ehsan; Valilou, Shirin

    2018-02-01

    In this paper, we have proposed a new online Wavelet Complementary velocity Estimator (WCE) over position and acceleration data gathered from an electro hydraulic servo shaking table. This is a batch estimator type that is based on the wavelet filter banks which extract the high and low resolution of data. The proposed complementary estimator combines these two resolutions of velocities which acquired from numerical differentiation and integration of the position and acceleration sensors by considering a fixed moving horizon window as input to wavelet filter. Because of using wavelet filters, it can be implemented in a parallel procedure. By this method the numerical velocity is estimated without having high noise of differentiators, integration drifting bias and with less delay which is suitable for active vibration control in high precision Mechatronics systems by Direct Velocity Feedback (DVF) methods. This method allows us to make velocity sensors with less mechanically moving parts which makes it suitable for fast miniature structures. We have compared this method with Kalman and Butterworth filters over stability, delay and benchmarked them by their long time velocity integration for getting back the initial position data. Copyright © 2017 ISA. Published by Elsevier Ltd. All rights reserved.

  16. High Throughput Transcriptomics @ USEPA (Toxicology ...

    Science.gov (United States)

    The ideal chemical testing approach will provide complete coverage of all relevant toxicological responses. It should be sensitive and specific It should identify the mechanism/mode-of-action (with dose-dependence). It should identify responses relevant to the species of interest. Responses should ideally be translated into tissue-, organ-, and organism-level effects. It must be economical and scalable. Using a High Throughput Transcriptomics platform within US EPA provides broader coverage of biological activity space and toxicological MOAs and helps fill the toxicological data gap. Slide presentation at the 2016 ToxForum on using High Throughput Transcriptomics at US EPA for broader coverage biological activity space and toxicological MOAs.

  17. Perilipin-2 Deletion Impairs Hepatic Lipid Accumulation by Interfering with Sterol Regulatory Element-binding Protein (SREBP) Activation and Altering the Hepatic Lipidome*

    Science.gov (United States)

    Libby, Andrew E.; Bales, Elise; Orlicky, David J.; McManaman, James L.

    2016-01-01

    Perilipin-2 (PLIN2) is a constitutively associated cytoplasmic lipid droplet coat protein that has been implicated in fatty liver formation in non-alcoholic fatty liver disease. Mice with or without whole-body deletion of perilipin-2 (Plin2-null) were fed either Western or control diets for 30 weeks. Perilipin-2 deletion prevents obesity and insulin resistance in Western diet-fed mice and dramatically reduces hepatic triglyceride and cholesterol levels in mice fed Western or control diets. Gene and protein expression studies reveal that PLIN2 deletion suppressed SREBP-1 and SREBP-2 target genes involved in de novo lipogenesis and cholesterol biosynthetic pathways in livers of mice on either diet. GC-MS lipidomics demonstrate that this reduction correlated with profound alterations in the hepatic lipidome with significant reductions in both desaturation and elongation of hepatic neutral lipid species. To examine the possibility that lipidomic actions of PLIN2 deletion contribute to suppression of SREBP activation, we isolated endoplasmic reticulum membrane fractions from long-term Western diet-fed wild type (WT) and Plin2-null mice. Lipidomic analyses reveal that endoplasmic reticulum membranes from Plin2-null mice are markedly enriched in ω-3 and ω-6 long-chain polyunsaturated fatty acids, which others have shown inhibit SREBP activation and de novo lipogenesis. Our results identify PLIN2 as a determinant of global changes in the hepatic lipidome and suggest the hypothesis that these actions contribute to SREBP-regulated de novo lipogenesis involved in non-alcoholic fatty liver disease. PMID:27679530

  18. Perilipin-2 Deletion Impairs Hepatic Lipid Accumulation by Interfering with Sterol Regulatory Element-binding Protein (SREBP) Activation and Altering the Hepatic Lipidome.

    Science.gov (United States)

    Libby, Andrew E; Bales, Elise; Orlicky, David J; McManaman, James L

    2016-11-11

    Perilipin-2 (PLIN2) is a constitutively associated cytoplasmic lipid droplet coat protein that has been implicated in fatty liver formation in non-alcoholic fatty liver disease. Mice with or without whole-body deletion of perilipin-2 (Plin2-null) were fed either Western or control diets for 30 weeks. Perilipin-2 deletion prevents obesity and insulin resistance in Western diet-fed mice and dramatically reduces hepatic triglyceride and cholesterol levels in mice fed Western or control diets. Gene and protein expression studies reveal that PLIN2 deletion suppressed SREBP-1 and SREBP-2 target genes involved in de novo lipogenesis and cholesterol biosynthetic pathways in livers of mice on either diet. GC-MS lipidomics demonstrate that this reduction correlated with profound alterations in the hepatic lipidome with significant reductions in both desaturation and elongation of hepatic neutral lipid species. To examine the possibility that lipidomic actions of PLIN2 deletion contribute to suppression of SREBP activation, we isolated endoplasmic reticulum membrane fractions from long-term Western diet-fed wild type (WT) and Plin2-null mice. Lipidomic analyses reveal that endoplasmic reticulum membranes from Plin2-null mice are markedly enriched in ω-3 and ω-6 long-chain polyunsaturated fatty acids, which others have shown inhibit SREBP activation and de novo lipogenesis. Our results identify PLIN2 as a determinant of global changes in the hepatic lipidome and suggest the hypothesis that these actions contribute to SREBP-regulated de novo lipogenesis involved in non-alcoholic fatty liver disease. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

  19. Narrative journalism as complementary inquiry

    Directory of Open Access Journals (Sweden)

    Jørgen Jeppesen

    2011-10-01

    Full Text Available Narrative journalism is a method to craft stories worth reading about real people. In this article, we explore the ability of that communicative power to produce insights complementary to those obtainable through traditional qualitative and quantitative research methods. With examples from a study of journalistic narrative as patient involvement in professional rehabilitation, interview data transcribed as stories are analyzed for qualities of heterogeneity, sensibility, transparency, and reflexivity. Building on sociological theories of thinking with stories, writing as inquiry, and public journalism as ethnography, we suggest that narrative journalism as a common practice might unfold dimensions of subjective otherness of the self. Aspiring to unite writing in both transparently confrontational and empathetically dialogic ways, the narrative journalistic method holds a potential to expose dynamics of power within the interview.

  20. Identification of the lipid biomarkers from plasma in idiopathic pulmonary fibrosis by Lipidomics.

    Science.gov (United States)

    Yan, Feng; Wen, Zhensong; Wang, Rui; Luo, Wenling; Du, Yufeng; Wang, Wenjun; Chen, Xianyang

    2017-12-06

    Idiopathic pulmonary fibrosis (IPF) is an irreversible interstitial pulmonary disease featured by high mortality, chronic and progressive course, and poor prognosis with unclear etiology. Currently, more studies have been focusing on identifying biomarkers to predict the progression of IPF, such as genes, proteins, and lipids. Lipids comprise diverse classes of molecules and play a critical role in cellular energy storage, structure, and signaling. The role of lipids in respiratory diseases, including cystic fibrosis, asthma and chronic obstructive pulmonary disease (COPD) has been investigated intensely in the recent years. The human serum lipid profiles in IPF patients however, have not been thoroughly understood and it will be very helpful if there are available molecular biomarkers, which can be used to monitor the disease progression or provide prognostic information for IPF disease. In this study, we performed the ultraperformance liquid chromatography coupled with quadrupole time of flight mass spectrometry (UPLC-QTOF/MS) to detect the lipid variation and identify biomarker in plasma of IPF patients. The plasma were from 22 IPF patients before received treatment and 18 controls. A total of 507 individual blood lipid species were determined with lipidomics from the 40 plasma samples including 20 types of fatty acid, 159 types of glycerolipids, 221 types of glycerophospholipids, 47 types of sphingolipids, 46 types of sterol lipids, 7 types of prenol lipids, 3 types of saccharolipids, and 4 types of polyketides. By comparing the variations in the lipid metabolite levels in IPF patients, a total of 62 unique lipids were identified by statistical analysis including 24 kinds of glycerophoslipids, 30 kinds of glycerolipids, 3 kinds of sterol lipids, 4 kinds of sphingolipids and 1 kind of fatty acids. Finally, 6 out of 62 discriminating lipids were selected as the potential biomarkers, which are able to differentiate between IPF disease and controls with ROC

  1. Methyl Jasmonate-Induced Lipidomic and Biochemical Alterations in the Intertidal Macroalga Gracilaria dura (Gracilariaceae, Rhodophyta).

    Science.gov (United States)

    Kumari, Puja; Reddy, C R K; Jha, Bhavanath

    2015-10-01

    The role of exogenously added methyl jasmonate (MeJA), a lipid-derived signaling compound, in inducing oxidative stress in the marine red macroalga Gracilaria dura was investigated. MeJA at a concentration of 1-100 µM was a strong stimulant of reactive oxygen species (H(2)O(2), HO· and O(2) (·-)) (P < 0.05) causing considerable oxidative stress in G. dura. This further led to lipid peroxidation and degradation of the pigments Chl a and phycocyanin, with a concomitant increase in phycoerythrin. The MeJA-induced oxidative burst also led to the induction of a fatty acid oxidation cascade, resulting in the synthesis of hydroxy-oxylipins and the up-regulation of the 13-lipoxygenase pathway. Electrospray ionization-mass spectrometry-based shotgun lipidomic analysis revealed that monogalactosyldiacylglycerol (a chloroplastic glycerolipid) and phosphatidylcholine (extrachloroplastidic phopholipid) were the most affected lipid classes. The degradation of 18:3-fatty acid-containing monogalactosyldiacylglycerol inferred that it provided fatty acyl chains for the biosynthesis of 13-hydroperoxylinolenic acid, which was further directed towards either the jasmonate pathway or other alternative pathways of the fatty acid oxidation cascade, analogous to higher plants. Also, G. dura modulated the lipid acyl chains in such a way that no significant change was observed in the fatty acid profile of the treated thalli as compared with those of the control, except for C16:0, C16:1 (n-9), C20:3 (n-6) and C20:4 (n-6) (P < 0.05). Furthermore, MeJA caused the accumulation of phenolic compounds and the up-regulation of enzymes involved in secondary metabolism such as polyphenol oxidase, shikimate dehydrogenase and phenylalanine ammonia-lyase, indicating a shift towards secondary metabolism as a defense strategy to combat the induced oxidative stress. © The Author 2015. Published by Oxford University Press on behalf of Japanese Society of Plant Physiologists. All rights reserved. For

  2. Complementary medicine in chronic pain treatment.

    Science.gov (United States)

    Simpson, Charles A

    2015-05-01

    This article discusses several issues related to therapies that are considered "complementary" or "alternative" to conventional medicine. A definition of "complementary and alternative medicine" (CAM) is considered in the context of the evolving health care field of complementary medicine. A rationale for pain physicians and clinicians to understand these treatments of chronic pain is presented. The challenges of an evidence-based approach to incorporating CAM therapies are explored. Finally, a brief survey of the evidence that supports several widely available and commonly used complementary therapies for chronic pain is provided. Copyright © 2015 Elsevier Inc. All rights reserved.

  3. Special Section: Complementary and Alternative Medicine (CAM):Quiz on Complementary and Alternative Medicine

    Science.gov (United States)

    ... Special Section CAM Quiz on Complementary and Alternative Medicine Past Issues / Winter 2009 Table of Contents For ... low back pain. True False Complementary and alternative medicine (CAM) includes: Meditation Chiropractic Use of natural products, ...

  4. Effects of Stigmasterol and β-Sitosterol on Nonalcoholic Fatty Liver Disease in a Mouse Model: A Lipidomic Analysis.

    Science.gov (United States)

    Feng, Simin; Gan, Ling; Yang, Chung S; Liu, Anna B; Lu, Wenyun; Shao, Ping; Dai, Zhuqing; Sun, Peilong; Luo, Zisheng

    2018-04-04

    To study the effects of stigmasterol and β-sitosterol on high-fat Western diet (HFWD)-induced nonalcoholic fatty liver disease (NAFLD), lipidomic analyses were conducted in liver samples collected after 33 weeks of the treatment. Principal component analysis showed these phytosterols were effective in protecting against HFWD-induced NAFLD. Orthogonal projections to latent structures-discriminate analysis (OPLS-DA) and S-plots showed that triacylglycerols (TGs), phosphatidylcholines, cholesteryl esters, diacylglycerols, and free fatty acids (FFAs) were the major lipid species contributing to these discriminations. The alleviation of NAFLD is mainly associated with decreases in hepatic cholesterol, TGs with polyunsaturated fatty acids, and alterations of free hepatic FFA. In conclusion, phytosterols, at a dose comparable to that suggested for humans by the FDA for the reduction of plasma cholesterol levels, are shown to protect against NAFLD in this long-term (33-week) study.

  5. Roux-en-Y Gastric Bypass Surgery Induces Early Plasma Metabolomic and Lipidomic Alterations in Humans Associated with Diabetes Remission

    DEFF Research Database (Denmark)

    Arora, Tulika; Velagapudi, Vidya; Pournaras, Dimitri J

    2015-01-01

    -surgery levels. At 4 days after surgery, insulin levels correlated positively with metabolites of branched chain and aromatic amino acid metabolism and negatively with triglycerides with long-chain fatty acids. Of the 14 subjects with diabetes prior to surgery, 7 were in remission 2 years after surgery....... The subjects in remission displayed higher pre-surgery levels of tricarboxylic acid cycle intermediates and triglycerides with long-chain fatty acids compared with subjects not in remission. Thus, metabolic alterations are induced soon after surgery and subjects with diabetes remission differ in the metabolic......Roux-en-Y gastric bypass (RYGB) is an effective method to attain sustained weight loss and diabetes remission. We aimed to elucidate early changes in the plasma metabolome and lipidome after RYGB. Plasma samples from 16 insulin-resistant morbidly obese subjects, of whom 14 had diabetes, were...

  6. A Healthy Nordic Diet Alters the Plasma Lipidomic Profile in Adults with Features of Metabolic Syndrome in a Multicenter Randomized Dietary Intervention.

    Science.gov (United States)

    Lankinen, Maria; Schwab, Ursula; Kolehmainen, Marjukka; Paananen, Jussi; Nygren, Heli; Seppänen-Laakso, Tuulikki; Poutanen, Kaisa; Hyötyläinen, Tuulia; Risérus, Ulf; Savolainen, Markku J; Hukkanen, Janne; Brader, Lea; Marklund, Matti; Rosqvist, Fredrik; Hermansen, Kjeld; Cloetens, Lieselotte; Önning, Gunilla; Thorsdottir, Inga; Gunnarsdottir, Ingibjorg; Åkesson, Björn; Dragsted, Lars Ove; Uusitupa, Matti; Orešič, Matej

    2016-03-09

    A healthy Nordic diet is associated with improvements in cardiometabolic risk factors, but the effect on lipidomic profile is not known. The aim was to investigate how a healthy Nordic diet affects the fasting plasma lipidomic profile in subjects with metabolic syndrome. Men and women (n = 200) with features of metabolic syndrome [mean age: 55 y; body mass index (in kg/m 2 ): 31.6] were randomly assigned to either a healthy Nordic (n = 104) or a control (n = 96) diet for 18 or 24 wk at 6 centers. Of the participants, 156 completed the study with plasma lipidomic measurements. The healthy Nordic diet consisted of whole grains, fruits, vegetables, berries, vegetable oils and margarines, fish, low-fat milk products, and low-fat meat. An average Nordic diet served as the control diet and included low-fiber cereal products, dairy fat-based spreads, regular-fat milk products, and a limited amount of fruits, vegetables, and berries. Lipidomic profiles were measured at baseline, week 12, and the end of the intervention (18 or 24 wk) by using ultraperformance liquid chromatography mass spectrometry. The effects of the diets on the lipid variables were analyzed with linear mixed-effects models. Data from centers with 18- or 24-wk duration were also analyzed separately. Changes in 21 plasma lipids differed significantly between the groups at week 12 (false discovery rate P Nordic diet group compared with the control group. At the end of the study, changes in lipidomic profiles did not differ between the groups. However, when the intervention lasted 24 wk, changes in 8 plasma lipids that had been identified at 12 wk, including plasmalogens, were sustained. There were no differences in changes in plasma lipids between groups with an intervention of 18 wk. By the dietary biomarker score, adherence to diet did not explain the difference in the results related to the duration of the study. A healthy Nordic diet transiently modified the plasma lipidomic profile, specifically by

  7. Qualitative content analysis of complementary topical therapies ...

    African Journals Online (AJOL)

    In order to alleviate diabetic foot problems, patients sometimes seek complementary therapies outside the professional context. This paper describes the use of complementary remedies as a topical treatment for diabetic foot ulcers among Jordanians. Qualitative content analysis was used to analyse written responses of 68 ...

  8. Roux-en-Y Gastric Bypass Surgery Induces Early Plasma Metabolomic and Lipidomic Alterations in Humans Associated with Diabetes Remission.

    Directory of Open Access Journals (Sweden)

    Tulika Arora

    Full Text Available Roux-en-Y gastric bypass (RYGB is an effective method to attain sustained weight loss and diabetes remission. We aimed to elucidate early changes in the plasma metabolome and lipidome after RYGB. Plasma samples from 16 insulin-resistant morbidly obese subjects, of whom 14 had diabetes, were subjected to global metabolomics and lipidomics analysis at pre-surgery and 4 and 42 days after RYGB. Metabolites and lipid species were compared between time points and between subjects who were in remission and not in remission from diabetes 2 years after surgery. We found that the variables that were most discriminatory between time points were decanoic acid and octanoic acid, which were elevated 42 days after surgery, and sphingomyelins (18:1/21:0 and 18:1/23:3, which were at their lowest level 42 days after surgery. Insulin levels were lower at 4 and 42 days after surgery compared with pre-surgery levels. At 4 days after surgery, insulin levels correlated positively with metabolites of branched chain and aromatic amino acid metabolism and negatively with triglycerides with long-chain fatty acids. Of the 14 subjects with diabetes prior to surgery, 7 were in remission 2 years after surgery. The subjects in remission displayed higher pre-surgery levels of tricarboxylic acid cycle intermediates and triglycerides with long-chain fatty acids compared with subjects not in remission. Thus, metabolic alterations are induced soon after surgery and subjects with diabetes remission differ in the metabolic profiles at pre- and early post-surgery time points compared to patients not in remission.

  9. Valorization of Lipids from Gracilaria sp. through Lipidomics and Decoding of Antiproliferative and Anti-Inflammatory Activity

    Directory of Open Access Journals (Sweden)

    Elisabete da Costa

    2017-03-01

    Full Text Available The lipidome of the red seaweed Gracilaria sp., cultivated on land-based integrated multitrophic aquaculture (IMTA system, was assessed for the first time using hydrophilic interaction liquid chromatography-mass spectrometry and tandem mass spectrometry (HILIC–MS and MS/MS. One hundred and forty-seven molecular species were identified in the lipidome of the Gracilaria genus and distributed between the glycolipids classes monogalactosyl diacylglyceride (MGDG, digalactosyl diacylglyceride (DGDG, sulfoquinovosyl monoacylglyceride (SQMG, sulfoquinovosyl diacylglyceride (SQDG, the phospholipids phosphatidylcholine (PC, lyso-PC, phosphatidylglycerol (PG, lyso-PG, phosphatidylinositol (PI, phosphatidylethanolamine (PE, phosphatic acid (PA, inositolphosphoceramide (IPC, and betaine lipids monoacylglyceryl- and diacylglyceryl-N,N,N-trimethyl homoserine (MGTS and DGTS. Antiproliferative and anti-inflammatory effects promoted by lipid extract of Gracilaria sp. were evaluated by monitoring cell viability in human cancer lines and by using murine macrophages, respectively. The lipid extract decreased cell viability of human T-47D breast cancer cells and of 5637 human bladder cancer cells (estimated half-maximal inhibitory concentration (IC50 of 12.2 μg/mL and 12.9 μg/mL, respectively and inhibited the production of nitric oxide (NO evoked by the Toll-like receptor 4 agonist lipopolysaccharide (LPS on the macrophage cell line RAW 264.7 (35% inhibition at a concentration of 100 μg/mL. These findings contribute to increase the ranking in the value-chain of Gracilaria sp. biomass cultivated under controlled conditions on IMTA systems.

  10. Complementary therapies for acne vulgaris

    Science.gov (United States)

    Cao, Huijuan; Yang, Guoyan; Wang, Yuyi; Liu, Jian Ping; Smith, Caroline A; Luo, Hui; Liu, Yueming

    2015-01-01

    Background Acne is a chronic skin disease characterised by inflamed spots and blackheads on the face, neck, back, and chest. Cysts and scarring can also occur, especially in more severe disease. People with acne often turn to complementary and alternative medicine (CAM), such as herbal medicine, acupuncture, and dietary modifications, because of their concerns about the adverse effects of conventional medicines. However, evidence for CAM therapies has not been systematically assessed. Objectives To assess the effects and safety of any complementary therapies in people with acne vulgaris. Search methods We searched the following databases from inception up to 22 January 2014: the Cochrane Skin Group Specialised Register, the Cochrane Central Register of Controlled Trials (CENTRAL; 2014, Issue 1), MEDLINE (from 1946), Embase (from 1974), PsycINFO (from 1806), AMED (from 1985), CINAHL (from 1981), Scopus (from 1966), and a number of other databases listed in the Methods section of the review. The Cochrane CAM Field Specialised Register was searched up to May 2014. We also searched five trials registers and checked the reference lists of articles for further references to relevant trials. Selection criteria We included parallel-group randomised controlled trials (or the first phase data of randomised cross-over trials) of any kind of CAM, compared with no treatment, placebo, or other active therapies, in people with a diagnosis of acne vulgaris. Data collection and analysis Three authors collected data from each included trial and evaluated the methodological quality independently. They resolved disagreements by discussion and, as needed, arbitration by another author. Main results We included 35 studies, with a total of 3227 participants. We evaluated the majority as having unclear risk of selection, attrition, reporting, detection, and other biases. Because of the clinical heterogeneity between trials and the incomplete data reporting, we could only include four

  11. Complementary therapies for acne vulgaris.

    Science.gov (United States)

    Cao, Huijuan; Yang, Guoyan; Wang, Yuyi; Liu, Jian Ping; Smith, Caroline A; Luo, Hui; Liu, Yueming

    2015-01-19

    Acne is a chronic skin disease characterised by inflamed spots and blackheads on the face, neck, back, and chest. Cysts and scarring can also occur, especially in more severe disease. People with acne often turn to complementary and alternative medicine (CAM), such as herbal medicine, acupuncture, and dietary modifications, because of their concerns about the adverse effects of conventional medicines. However, evidence for CAM therapies has not been systematically assessed. To assess the effects and safety of any complementary therapies in people with acne vulgaris. We searched the following databases from inception up to 22 January 2014: the Cochrane Skin Group Specialised Register, the Cochrane Central Register of Controlled Trials (CENTRAL; 2014,Issue 1), MEDLINE (from 1946), Embase (from 1974), PsycINFO (from 1806), AMED (from 1985), CINAHL (from 1981), Scopus (from 1966), and a number of other databases listed in the Methods section of the review. The Cochrane CAM Field Specialised Register was searched up to May 2014. We also searched five trials registers and checked the reference lists of articles for further references to relevant trials. We included parallel-group randomised controlled trials (or the first phase data of randomised cross-over trials) of any kind of CAM, compared with no treatment, placebo, or other active therapies, in people with a diagnosis of acne vulgaris. Three authors collected data from each included trial and evaluated the methodological quality independently. They resolved disagreements by discussion and, as needed, arbitration by another author. We included 35 studies, with a total of 3227 participants. We evaluated the majority as having unclear risk of selection, attrition, reporting, detection, and other biases. Because of the clinical heterogeneity between trials and the incomplete data reporting, we could only include four trials in two meta-analyses, with two trials in each meta-analysis. The categories of CAM included

  12. Using precursor ion scan of 184 with liquid chromatography-electrospray ionization-tandem mass spectrometry for concentration normalization in cellular lipidomic studies.

    Science.gov (United States)

    Chao, Hsi-Chun; Chen, Guan-Yuan; Hsu, Lih-Ching; Liao, Hsiao-Wei; Yang, Sin-Yu; Wang, San-Yuan; Li, Yu-Liang; Tang, Sung-Chun; Tseng, Yufeng Jane; Kuo, Ching-Hua

    2017-06-08

    Cellular lipidomic studies have been favored approaches in many biomedical research areas. To provide fair comparisons of the studied cells, it is essential to perform normalization of the determined concentration before lipidomic analysis. This study proposed a cellular lipidomic normalization method by measuring the phosphatidylcholine (PC) and sphingomyelin (SM) contents in cell extracts. To provide efficient analysis of PC and SM in cell extracts, flow injection analysis-electrospray ionization-tandem mass spectrometry (FIA-ESI-MS/MS) with a precursor ion scan (PIS) of m/z 184 was used, and the parameters affecting the performance of the method were optimized. Good linearity could be observed between the cell extract dilution factor and the reciprocal of the total ion chromatogram (TIC) area in the PIS of m/z 184 within the dilution range of 1- to 16-fold (R 2  = 0.998). The calibration curve could be used for concentration adjustment of the unknown concentration of a cell extract. The intraday and intermediate precisions were below 10%. The accuracy ranged from 93.0% to 105.6%. The performance of the new normalization method was evaluated using different numbers of HCT-116 cells. Sphingosine, ceramide (d18:1/18:0), SM (d18:1/18:0) and PC (16:1/18:0) were selected as the representative test lipid species, and the results showed that the peak areas of each lipid species obtained from different cell numbers were within a 20% variation after normalization. Finally, the PIS of 184 normalization method was applied to study ischemia-induced neuron injury using oxygen and glucose deprivation (OGD) on primary neuronal cultured cells. Our results showed that the PIS of 184 normalization method is an efficient and effective approach for concentration normalization in cellular lipidomic studies. Copyright © 2017 Elsevier B.V. All rights reserved.

  13. The lipidome in major depressive disorder: Shared genetic influence for ether-phosphatidylcholines, a plasma-based phenotype related to inflammation, and disease risk.

    Science.gov (United States)

    Knowles, E E M; Huynh, K; Meikle, P J; Göring, H H H; Olvera, R L; Mathias, S R; Duggirala, R; Almasy, L; Blangero, J; Curran, J E; Glahn, D C

    2017-06-01

    The lipidome is rapidly garnering interest in the field of psychiatry. Recent studies have implicated lipidomic changes across numerous psychiatric disorders. In particular, there is growing evidence that the concentrations of several classes of lipids are altered in those diagnosed with MDD. However, for lipidomic abnormalities to be considered potential treatment targets for MDD (rather than secondary manifestations of the disease), a shared etiology between lipid concentrations and MDD should be demonstrated. In a sample of 567 individuals from 37 extended pedigrees (average size 13.57 people, range=3-80), we used mass spectrometry lipidomic measures to evaluate the genetic overlap between twenty-three biologically distinct lipid classes and a dimensional scale of MDD. We found that the lipid class with the largest endophenotype ranking value (ERV, a standardized parametric measure of pleiotropy) were ether-phosphodatidylcholines (alkylphosphatidylcholine, PC(O) and alkenylphosphatidylcholine, PC(P) subclasses). Furthermore, we examined the cluster structure of the twenty-five species within the top-ranked lipid class, and the relationship of those clusters with MDD. This analysis revealed that species containing arachidonic acid generally exhibited the greatest degree of genetic overlap with MDD. This study is the first to demonstrate a shared genetic etiology between MDD and ether-phosphatidylcholine species containing arachidonic acid, an omega-6 fatty acid that is a precursor to inflammatory mediators, such as prostaglandins. The study highlights the potential utility of the well-characterized linoleic/arachidonic acid inflammation pathway as a diagnostic marker and/or treatment target for MDD. Copyright © 2017 Elsevier Masson SAS. All rights reserved.

  14. Investigating the Correspondence Between Transcriptomic and Proteomic Expression Profiles Using Coupled Cluster Models

    International Nuclear Information System (INIS)

    Rogers, Simon; Girolami, Mark; Kolch, Walter; Waters, Katrina M.; Liu, Tao; Thrall, Brian D.; Wiley, H. S.

    2008-01-01

    correspondence between mRNA and protein expression. The exceptions involve a few selected multi-protein complexes that require the stoichiometric expression of components for correct function. This finding has wide ramifications regarding the understanding of gene and protein expression including its control and evolution. It also shows that transcriptomic and proteomic expression analysis are complementary and non-redundant

  15. Corporates Governance: A complementary model for multi ...

    African Journals Online (AJOL)

    pc

    2018-03-05

    Mar 5, 2018 ... Architecture" with a complementary framework is important to make sure for ... Research Article. Special Issue ... complimentary is that it helps in providing a lot of Metrics which are very useful .... Data quality. • Data priority ...

  16. complementary techniques of percutaneous closure of ductus

    African Journals Online (AJOL)

    2013-07-07

    Jul 7, 2013 ... the complementary use of either type of devices to close small and ... complete occlusion of the ductus. 2F ... release of the device showing complete occlusion. 3E ..... Raskinds prosthesis Circulation 1989; 80:1706-1710 . 5.

  17. Irritable Bowel Syndrome and Complementary Health Practices

    Science.gov (United States)

    ... IBS) in adults: conventional and complementary/alternative approaches. Alternative Medicine Review. 2011;16(2):134–151. Herbal Supplements Shi J, Tong Y, Shen JG, et al. Effectiveness and safety of herbal medicines in the treatment ...

  18. African Journal of Traditional, Complementary and Alternative ...

    African Journals Online (AJOL)

    African Journal of Traditional, Complementary and Alternative Medicines. ... and Ficus thonningii blume (moraceae), two plants used in traditional medicine in the ... The effective method for investigation meridian tropism theory in rats · EMAIL ...

  19. Corporates governance: a complementary model for multi ...

    African Journals Online (AJOL)

    Corporates governance: a complementary model for multi frameworks and tools. ... Organization became highly needed to transform and convert the available legacy of fragmented solutions and ... Also Data considered as a vital part of the .

  20. Complementary DNA-amplified fragment length polymorphism ...

    African Journals Online (AJOL)

    Complementary DNA-amplified fragment length polymorphism (AFLP-cDNA) analysis of differential gene expression from the xerophyte Ammopiptanthus mongolicus in response to cold, drought and cold together with drought.

  1. African Journal of Traditional, Complementary and Alternative ...

    African Journals Online (AJOL)

    African Journal of Traditional, Complementary and Alternative Medicines. ... based on a descriptive survey from the western black sea region of Turkey · EMAIL ... on volatile oil constituents of Codonopsis radix (dangshen) by GC-MS method ...

  2. African Journal of Traditional, Complementary and Alternative ...

    African Journals Online (AJOL)

    African Journal of Traditional, Complementary and Alternative Medicines. ... extracts of three Togolese medicinal plants against ESBL Klebsiella pneumoniae strains ... Ethnobotanical survey of medicinal plants used in the management of ...

  3. Alternative and Complementary Therapies for Hepatitis C

    Science.gov (United States)

    ... and Complementary Therapies Viral Hepatitis Menu Menu Viral Hepatitis Viral Hepatitis Home For Veterans and the Public Veterans ... treatments which have been proven to reduce the hepatitis C viral load. Just because something is "natural" (an herb, ...

  4. African Journal of Traditional, Complementary and Alternative ...

    African Journals Online (AJOL)

    These observations could be explained by some qualitative and /or quantitative differences observed between the constituents of the two essential oils studied. Keywords: Cymbopogon nardus, Essential oil, Chemistry, Analgesic, Comparison, Benin, Congo. African Journal of Traditional and Complementary Medicine Vol.

  5. African Journal of Traditional, Complementary and Alternative ...

    African Journals Online (AJOL)

    AJTCAM), a new broad-based journal, is founded on two key tenets: To publish exciting research in all areas of applied medicinal plants, Traditional medicines, Complementary Alternative Medicines, food and agricultural technologies, and ...

  6. Strategic and Operational Plan for Integrating Transcriptomics ...

    Science.gov (United States)

    Plans for incorporating high throughput transcriptomics into the current high throughput screening activities at NCCT; the details are in the attached slide presentation presentation on plans for incorporating high throughput transcriptomics into the current high throughput screening activities at NCCT, given at the OECD meeting on June 23, 2016

  7. Detraditionalisation, gender and alternative and complementary medicines.

    Science.gov (United States)

    Sointu, Eeva

    2011-03-01

    This article is premised on the importance of locating the appeal and meaning of alternative and complementary medicines in the context of gendered identities. I argue that the discourse of wellbeing--captured in many alternative and complementary health practices--is congruent with culturally prevalent ideals of self-fulfilling, authentic, unique and self-responsible subjectivity. The discourse of wellbeing places the self at the centre, thus providing a contrast with traditional ideas of other-directed and caring femininity. As such, involvement in alternative and complementary medicines is entwined with a negotiation of shifting femininities in detraditionalising societies. Simultaneously, many alternative and complementary health practices readily tap into and reproduce traditional representations of caring femininity. It is through an emphasis on emotional honesty and intimacy that the discourse of wellbeing also captures a challenge to traditional ideas of masculinity. Expectations and experiences relating to gender add a further level of complexity to the meaningfulness and therapeutic value of alternative and complementary medicines and underlie the gender difference in the utilisation of holistic health practices. I draw on data from a qualitative study with 44, primarily white, middle-class users and practitioners of varied alternative and complementary medicines in the UK. © 2010 The Author. Sociology of Health & Illness © 2010 Foundation for the Sociology of Health & Illness/Blackwell Publishing Ltd.

  8. Comparative plasma lipidome between human and cynomolgus monkey: are plasma polar lipids good biomarkers for diabetic monkeys?

    Directory of Open Access Journals (Sweden)

    Guanghou Shui

    Full Text Available BACKGROUND: Non-human primates (NHP are now being considered as models for investigating human metabolic diseases including diabetes. Analyses of cholesterol and triglycerides in plasma derived from NHPs can easily be achieved using methods employed in humans. Information pertaining to other lipid species in monkey plasma, however, is lacking and requires comprehensive experimental analysis. METHODOLOGIES/PRINCIPAL FINDINGS: We examined the plasma lipidome from 16 cynomolgus monkey, Macaca fascicularis, using liquid chromatography coupled with mass spectrometry (LC/MS. We established novel analytical approaches, which are based on a simple gradient elution, to quantify polar lipids in plasma including (i glycerophospholipids (phosphatidylcholine, PC; phosphatidylethanolamine, PE; phosphatidylinositol, PI; phosphatidylglycerol, PG; phosphatidylserine, PS; phosphatidic acid, PA; (ii sphingolipids (sphingomyelin, SM; ceramide, Cer; Glucocyl-ceramide, GluCer; ganglioside mannoside 3, GM3. Lipidomic analysis had revealed that the plasma of human and cynomolgus monkey were of similar compositions, with PC, SM, PE, LPC and PI constituting the major polar lipid species present. Human plasma contained significantly higher levels of plasmalogen PE species (p<0.005 and plasmalogen PC species (p<0.0005, while cynomolgus monkey had higher levels of polyunsaturated fatty acyls (PUFA in PC, PE, PS and PI. Notably, cynomolgus monkey had significantly lower levels of glycosphingolipids, including GluCer (p<0.0005 and GM(3 (p<0.0005, but higher level of Cer (p<0.0005 in plasma than human. We next investigated the biochemical alterations in blood lipids of 8 naturally occurring diabetic cynomolgus monkeys when compared with 8 healthy controls. CONCLUSIONS: For the first time, we demonstrated that the plasma of human and cynomolgus monkey were of similar compositions, but contained different mol distribution of individual molecular species. Diabetic monkeys

  9. Immunometabolic and Lipidomic Markers Associated With the Frailty Index and Quality of Life in Aging HIV+ Men on Antiretroviral Therapy

    Directory of Open Access Journals (Sweden)

    Hui-Ling Yeoh

    2017-08-01

    Full Text Available Chronic immune activation persists despite antiretroviral therapy (ART in HIV+ individuals and underpins an increased risk of age-related co-morbidities. We assessed the Frailty Index in older HIV+ Australian men on ART. Immunometabolic markers on monocytes and T cells were analyzed using flow cytometry, plasma innate immune activation markers by ELISA, and lipidomic profiling by mass spectrometry. The study population consisted of 80 HIV+ men with a median age of 59 (IQR, 56–65, and most had an undetectable viral load (92%. 24% were frail, and 76% were non-frail. Frailty was associated with elevated Glucose transporter-1 (Glut1 expression on the total monocytes (p = 0.04, increased plasma levels of innate immune activation marker sCD163 (OR, 4.8; CI 1.4–15.9, p = 0.01, phosphatidylethanolamine PE(36:3 (OR, 5.1; CI 1.7–15.5, p = 0.004 and triacylglycerol TG(16:1_18:1_18:1 (OR, 3.4; CI 1.3–9.2, p = 0.02, but decreased expression of GM3 ganglioside, GM3(d18:1/18:0 (OR, 0.1; CI 0.0–0.6, p = 0.01 and monohexosylceramide HexCerd(d18:1/22:0 (OR, 0.1; CI 0.0–0.5, p = 0.004. There is a strong inverse correlation between quality of life and the concentration of PE(36:3 (ρ = −0.33, p = 0.004 and PE(36:4 (ρ = −0.37, p = 0.001. These data suggest that frailty is associated with increased innate immune activation and abnormal lipidomic profile. These markers should be investigated in larger, longitudinal studies to determine their potential as biomarkers for frailty.

  10. Transcriptomic signatures in cartilage ageing

    Science.gov (United States)

    2013-01-01

    Introduction Age is an important factor in the development of osteoarthritis. Microarray studies provide insight into cartilage aging but do not reveal the full transcriptomic phenotype of chondrocytes such as small noncoding RNAs, pseudogenes, and microRNAs. RNA-Seq is a powerful technique for the interrogation of large numbers of transcripts including nonprotein coding RNAs. The aim of the study was to characterise molecular mechanisms associated with age-related changes in gene signatures. Methods RNA for gene expression analysis using RNA-Seq and real-time PCR analysis was isolated from macroscopically normal cartilage of the metacarpophalangeal joints of eight horses; four young donors (4 years old) and four old donors (>15 years old). RNA sequence libraries were prepared following ribosomal RNA depletion and sequencing was undertaken using the Illumina HiSeq 2000 platform. Differentially expressed genes were defined using Benjamini-Hochberg false discovery rate correction with a generalised linear model likelihood ratio test (P ageing cartilage. Conclusion There was an age-related dysregulation of matrix, anabolic and catabolic cartilage factors. This study has increased our knowledge of transcriptional networks in cartilage ageing by providing a global view of the transcriptome. PMID:23971731

  11. Developmental transcriptome of Aplysia californica'

    KAUST Repository

    Heyland, Andreas

    2010-12-06

    Genome-wide transcriptional changes in development provide important insight into mechanisms underlying growth, differentiation, and patterning. However, such large-scale developmental studies have been limited to a few representatives of Ecdysozoans and Chordates. Here, we characterize transcriptomes of embryonic, larval, and metamorphic development in the marine mollusc Aplysia californica and reveal novel molecular components associated with life history transitions. Specifically, we identify more than 20 signal peptides, putative hormones, and transcription factors in association with early development and metamorphic stages-many of which seem to be evolutionarily conserved elements of signal transduction pathways. We also characterize genes related to biomineralization-a critical process of molluscan development. In summary, our experiment provides the first large-scale survey of gene expression in mollusc development, and complements previous studies on the regulatory mechanisms underlying body plan patterning and the formation of larval and juvenile structures. This study serves as a resource for further functional annotation of transcripts and genes in Aplysia, specifically and molluscs in general. A comparison of the Aplysia developmental transcriptome with similar studies in the zebra fish Danio rerio, the fruit fly Drosophila melanogaster, the nematode Caenorhabditis elegans, and other studies on molluscs suggests an overall highly divergent pattern of gene regulatory mechanisms that are likely a consequence of the different developmental modes of these organisms. © 2010 Wiley-Liss, Inc., A Wiley Company.

  12. [Complementary and alternative medicine in oncology].

    Science.gov (United States)

    Hübner, J

    2013-06-01

    Complementary and alternative medicine are frequently used by cancer patients. The main benefit of complementary medicine is that it gives patients the chance to become active. Complementary therapy can reduce the side effects of conventional therapy. However, we have to give due consideration to side effects and interactions: the latter being able to reduce the effectiveness of cancer therapy and so to jeopardise the success of therapy. Therefore, complementary therapy should be managed by the oncologist. It is based on a common concept of cancerogenesis with conventional therapy. Complement therapy can be assessed in studies. Alternative medicine in contrast rejects common rules of evidence-based medicine. It starts from its own concepts of cancerogenesis, which is often in line with the thinking of lay persons. Alternative medicine is offered as either "alternative" to recommended cancer treatment or is used at the same time but without due regard for the interactions. Alternative medicine is a high risk to patients. In the following two parts of the article, the most important complementary and alternative therapies cancer patients use nowadays are presented and assessed according to published evidence.

  13. Effects of sex, age, and fasting conditions on plasma lipidomic profiles of fasted Sprague-Dawley rats.

    Directory of Open Access Journals (Sweden)

    Kosuke Saito

    Full Text Available Circulating lipid molecules reflect biological processes in the body and, thus, are useful tools for preclinical estimation of the efficacy and safety of newly developed drugs. However, background information on profiles of circulating lipid molecules in preclinical animal models is limited. Therefore, we examined the effects of multiple factors such as sex (fasted male vs. female, age (fasted 10 vs. 30 weeks old, and feeding conditions (feeding vs. fasting, 16 vs. 22 hr fasting, 10 AM vs. 4 PM blood collection, on the global profiles of lipid molecules in plasma from Sprague-Dawley rats by using a lipidomic approach. Our assay platform determined 262 lipid molecules (68 phospholipids, 20 sphingolipids, 138 neutral lipids, and 36 polyunsaturated fatty acids and their metabolites in rat plasma. Multivariate discriminant analysis (orthogonal partial least squares discriminant analysis and heat maps of statistically significant lipid molecules revealed that the plasma lipid profiles in rats are predominantly influenced by feeding conditions, followed by sex and age. In addition, the fasting duration (16 vs. 22 hr fasting or the time of blood collection (10 AM vs. 4 PM blood collection has limited or no contribution on the profiles of lipid molecules in rat plasma. Our results provide useful, fundamental information for exploring and validating biomarkers in future preclinical studies and may help to establish regulatory standards for such studies.

  14. Combination of mass spectrometry-based targeted lipidomics and supervised machine learning algorithms in detecting adulterated admixtures of white rice.

    Science.gov (United States)

    Lim, Dong Kyu; Long, Nguyen Phuoc; Mo, Changyeun; Dong, Ziyuan; Cui, Lingmei; Kim, Giyoung; Kwon, Sung Won

    2017-10-01

    The mixing of extraneous ingredients with original products is a common adulteration practice in food and herbal medicines. In particular, authenticity of white rice and its corresponding blended products has become a key issue in food industry. Accordingly, our current study aimed to develop and evaluate a novel discrimination method by combining targeted lipidomics with powerful supervised learning methods, and eventually introduce a platform to verify the authenticity of white rice. A total of 30 cultivars were collected, and 330 representative samples of white rice from Korea and China as well as seven mixing ratios were examined. Random forests (RF), support vector machines (SVM) with a radial basis function kernel, C5.0, model averaged neural network, and k-nearest neighbor classifiers were used for the classification. We achieved desired results, and the classifiers effectively differentiated white rice from Korea to blended samples with high prediction accuracy for the contamination ratio as low as five percent. In addition, RF and SVM classifiers were generally superior to and more robust than the other techniques. Our approach demonstrated that the relative differences in lysoGPLs can be successfully utilized to detect the adulterated mixing of white rice originating from different countries. In conclusion, the present study introduces a novel and high-throughput platform that can be applied to authenticate adulterated admixtures from original white rice samples. Copyright © 2017 Elsevier Ltd. All rights reserved.

  15. High-resolution lipidomics coupled with rapid fixation reveals novel ischemia-induced signaling in the rat neurolipidome.

    Science.gov (United States)

    Trépanier, Marc-Olivier; Eiden, Michael; Morin-Rivron, Delphine; Bazinet, Richard P; Masoodi, Mojgan

    2017-03-01

    The field of lipidomics has evolved vastly since its creation 15 years ago. Advancements in mass spectrometry have allowed for the identification of hundreds of intact lipids and lipid mediators. However, because of the release of fatty acids from the phospholipid membrane in the brain caused by ischemia, identifying the neurolipidome has been challenging. Microwave fixation has been shown to reduce the ischemia-induced release of several lipid mediators. Therefore, this study aimed to develop a method combining high-resolution tandem mass spectrometry (MS/MS), high-energy head-focused microwave fixation and statistical modeling, allowing for the measurement of intact lipids and lipid mediators in order to eliminate the ischemia-induced release of fatty acids and identify the rat neurolipidome. In this study, we demonstrated the ischemia-induced production of bioactive lipid mediators, and the reduction in variability using microwave fixation in combination with liquid chromatography (LC)-MS/MS. We have also illustrated for the first time that microwave fixation eliminates the alterations in intact lipid species following ischemia. While many phospholipid species were unchanged by ischemia, other intact lipid classes, such as diacylglycerol, were lower in concentration following microwave fixation compared to ischemia. © 2016 International Society for Neurochemistry.

  16. Long-term increased carnitine palmitoyltransferase 1A expression in ventromedial hypotalamus causes hyperphagia and alters the hypothalamic lipidomic profile.

    Directory of Open Access Journals (Sweden)

    Paula Mera

    Full Text Available Lipid metabolism in the ventromedial hypothalamus (VMH has emerged as a crucial pathway in the regulation of feeding and energy homeostasis. Carnitine palmitoyltransferase (CPT 1A is the rate-limiting enzyme in mitochondrial fatty acid β-oxidation and it has been proposed as a crucial mediator of fasting and ghrelin orexigenic signalling. However, the relationship between changes in CPT1A activity and the intracellular downstream effectors in the VMH that contribute to appetite modulation is not fully understood. To this end, we examined the effect of long-term expression of a permanently activated CPT1A isoform by using an adeno-associated viral vector injected into the VMH of rats. Peripherally, this procedure provoked hyperghrelinemia and hyperphagia, which led to overweight, hyperglycemia and insulin resistance. In the mediobasal hypothalamus (MBH, long-term CPT1AM expression in the VMH did not modify acyl-CoA or malonyl-CoA levels. However, it altered the MBH lipidomic profile since ceramides and sphingolipids increased and phospholipids decreased. Furthermore, we detected increased vesicular γ-aminobutyric acid transporter (VGAT and reduced vesicular glutamate transporter 2 (VGLUT2 expressions, both transporters involved in this orexigenic signal. Taken together, these observations indicate that CPT1A contributes to the regulation of feeding by modulating the expression of neurotransmitter transporters and lipid components that influence the orexigenic pathways in VMH.

  17. Lipidomic data on lipid droplet triglyceride remodelling associated with protection of breast cancer cells from lipotoxic stress.

    Science.gov (United States)

    Jarc, Eva; Eichmann, Thomas O; Zimmermann, Robert; Petan, Toni

    2018-06-01

    The data presented here is related to the research article entitled "Lipid droplets induced by secreted phospholipase A 2 and unsaturated fatty acids protect breast cancer cells from nutrient and lipotoxic stress" by E. Jarc et al., Biochim. Biophys. Acta 1863 (2018) 247-265. Elevated uptake of unsaturated fatty acids and lipid droplet accumulation are characteristic of aggressive cancer cells and have been associated with the cellular stress response. The present study provides lipidomic data on the triacylglycerol (TAG) and phosphatidylcholine (PC) composition of MDA-MB-231 breast cancer cells exposed to docosahexaenoic acid (DHA; 22:6, ω-3). Datasets provide information on the changes in lipid composition induced by depletion of adipose triglyceride lipase (ATGL) and by exogenous addition of secreted phospholipase A 2 (sPLA 2 ) in DHA-treated cells. The presented alterations in lipid composition, mediated by targeting lipid droplet biogenesis and lipolysis, are associated with protection from lipotoxicity and allow further investigation into the role of lipid droplets in the resistance of cancer cells to lipotoxic stress.

  18. An integrated lipidomics and metabolomics reveal nephroprotective effect and biochemical mechanism of Rheum officinale in chronic renal failure

    Science.gov (United States)

    Zhang, Zhi-Hao; Vaziri, Nosratola D.; Wei, Feng; Cheng, Xian-Long; Bai, Xu; Zhao, Ying-Yong

    2016-01-01

    Chronic renal failure (CRF) is a major public health problem worldwide. Earlier studies have revealed salutary effects of rhubarb extracts in CRF. In this study, we employed lipidomic and metabolomic approaches to identify the plasma biomarkers and to determine the effect of treatment with petroleum ether, ethyl acetate and n-butanol extracts of rhubarb in a rat model of CRF with adenine-induced chronic tubulointerstitial nephropathy. In addition, clinical biochemistry, histological evaluation and pro-fibrotic protein expression were analyzed. Significant changes were found between the CRF and control groups representing characteristic phenotypes of rats with CRF. Treatment with the three rhubarb extracts improved renal injury and dysfunction, either fully or partially reversed the plasma metabolites abnormalities and attenuated upregulation of pro-fibrotic proteins including TGF-β1, α-SMA, PAI-1, CTGF, FN and collagen-1. The nephroprotective effect of ethyl acetate extract was better than other extracts. The differential metabolites were closely associated with glycerophospholipid, fatty acid and amino acid metabolisms. The results revealed a strong link between renal tubulointerstitial fibrosis and glycerophospholipid metabolism and L-carnitine metabolism in the development of CRF. Amelioration of CRF with the three rhubarb extracts was associated with the delayed development and/or reversal the disorders in key metabolites associated with adenine-induced CRF. PMID:26903149

  19. A Lipidomics Approach in the Characterization of Zika-Infected Mosquito Cells: Potential Targets for Breaking the Transmission Cycle.

    Directory of Open Access Journals (Sweden)

    Carlos Fernando Odir Rodrigues Melo

    Full Text Available Recent outbreaks of Zika virus in Oceania and Latin America, accompanied by unexpected clinical complications, made this infection a global public health concern. This virus has tropism to neural tissue, leading to microcephaly in newborns in a significant proportion of infected mothers. The clinical relevance of this infection, the difficulty to perform accurate diagnosis and the small amount of data in literature indicate the necessity of studies on Zika infection in order to characterize new biomarkers of this infection and to establish new targets for viral control in vertebrates and invertebrate vectors. Thus, this study aims at establishing a lipidomics profile of infected mosquito cells compared to a control group to define potential targets for viral control in mosquitoes. Thirteen lipids were elected as specific markers for Zika virus infection (Brazilian strain, which were identified as putatively linked to the intracellular mechanism of viral replication and/or cell recognition. Our findings bring biochemical information that may translate into useful targets for breaking the transmission cycle.

  20. Complementary structure for designer localized surface plasmons

    Science.gov (United States)

    Gao, Zhen; Gao, Fei; Zhang, Youming; Zhang, Baile

    2015-11-01

    Magnetic localized surface plasmons (LSPs) supported on metallic structures corrugated by very long and curved grooves have been recently proposed and demonstrated on an extremely thin metallic spiral structure (MSS) in the microwave regime. However, the mode profile for the magnetic LSPs was demonstrated by measuring only the electric field, not the magnetic field. Here, based on Babinet's principle, we propose a Babinet-inverted, or complementary MSS whose electric/magnetic mode profiles match the magnetic/electric mode profiles of MSS. This complementarity of mode profiles allows mapping the magnetic field distribution of magnetic LSP mode profile on MSS by measuring the electric field distribution of the corresponding mode on complementary MSS. Experiment at microwave frequencies also demonstrate the use of complementary MSS in sensing refractive-index change in the environment.

  1. Comparative transcriptomics in the Triticeae

    Directory of Open Access Journals (Sweden)

    Waugh Robbie

    2009-06-01

    Full Text Available Abstract Background Barley and particularly wheat are two grass species of immense agricultural importance. In spite of polyploidization events within the latter, studies have shown that genotypically and phenotypically these species are very closely related and, indeed, fertile hybrids can be created by interbreeding. The advent of two genome-scale Affymetrix GeneChips now allows studies of the comparison of their transcriptomes. Results We have used the Wheat GeneChip to create a "gene expression atlas" for the wheat transcriptome (cv. Chinese Spring. For this, we chose mRNA from a range of tissues and developmental stages closely mirroring a comparable study carried out for barley (cv. Morex using the Barley1 GeneChip. This, together with large-scale clustering of the probesets from the two GeneChips into "homologous groups", has allowed us to perform a genomic-scale comparative study of expression patterns in these two species. We explore the influence of the polyploidy of wheat on the results obtained with the Wheat GeneChip and quantify the correlation between conservation in gene sequence and gene expression in wheat and barley. In addition, we show how the conservation of expression patterns can be used to elucidate, probeset by probeset, the reliability of the Wheat GeneChip. Conclusion While there are many differences in expression on the level of individual genes and tissues, we demonstrate that the wheat and barley transcriptomes appear highly correlated. This finding is significant not only because given small evolutionary distance between the two species it is widely expected, but also because it demonstrates that it is possible to use the two GeneChips for comparative studies. This is the case even though their probeset composition reflects rather different design principles as well as, of course, the present incomplete knowledge of the gene content of the two species. We also show that, in general, the Wheat GeneChip is not able

  2. Characterizing the transcriptome and molecular markers information ...

    Indian Academy of Sciences (India)

    2008). Analyses of the genetic structure .... The annotations and classifications for the transcriptome ... Based on the Pfam classification, the predic- ..... J. Lipid. Res. 33, 251–262. Eckert C. G., Samis K. E. and Lougheed S. C. 2008 Genetic vari-.

  3. The floral transcriptome of Eucalyptus grandis

    CSIR Research Space (South Africa)

    Vining, KJ

    2015-10-01

    Full Text Available As a step toward functional annotation of genes required for floral initiation and development within the Eucalyptus genome, we used short read sequencing to analyze transcriptomes of floral buds from early and late developmental stages...

  4. Combined lipidomic and proteomic analysis of isolated human islets exposed to palmitate reveals time-dependent changes in insulin secretion and lipid metabolism.

    Directory of Open Access Journals (Sweden)

    Kirsten Roomp

    Full Text Available Studies on the pathophysiology of type 2 diabetes mellitus (T2DM have linked the accumulation of lipid metabolites to the development of beta-cell dysfunction and impaired insulin secretion. In most in vitro models of T2DM, rodent islets or beta-cell lines are used and typically focus is on specific cellular pathways or organs. Our aim was to, firstly, develop a combined lipidomics and proteomics approach for lipotoxicity in isolated human islets and, secondly, investigate if the approach could delineate novel and/ or confirm reported mechanisms of lipotoxicity. To this end isolated human pancreatic islets, exposed to chronically elevated palmitate concentrations for 0, 2 and 7 days, were functionally characterized and their levels of multiple targeted lipid and untargeted protein species determined. Glucose-stimulated insulin secretion from the islets increased on day 2 and decreased on day 7. At day 7 islet insulin content decreased and the proinsulin to insulin content ratio doubled. Amounts of cholesterol, stearic acid, C16 dihydroceramide and C24:1 sphingomyelin, obtained from the lipidomic screen, increased time-dependently in the palmitate-exposed islets. The proteomic screen identified matching changes in proteins involved in lipid biosynthesis indicating up-regulated cholesterol and lipid biosynthesis in the islets. Furthermore, proteins associated with immature secretory granules were decreased when palmitate exposure time was increased despite their high affinity for cholesterol. Proteins associated with mature secretory granules remained unchanged. Pathway analysis based on the protein and lipid expression profiles implicated autocrine effects of insulin in lipotoxicity. Taken together the study demonstrates that combining different omics approaches has potential in mapping of multiple simultaneous cellular events. However, it also shows that challenges exist for effectively combining lipidomics and proteomics in primary cells. Our

  5. 3rd International Conference on Transcriptomics

    OpenAIRE

    John A Daniel

    2017-01-01

    Conference Series has been instrumental in conducting international Biochemistry meetings for seven years, and very excited to expand Europe, America and Asia Pacific continents. Previous meetings were held in major cities like Philadelphia, Orlando with success the meetings again scheduled in three continents. 3rd International Conference on Transcriptomics to be held during October 30 - November 01, 2017 at Bangkok, Thailand The Global Transcriptomics business sector to develop at a C...

  6. Black Hole Complementary Principle and Noncommutative Membrane

    International Nuclear Information System (INIS)

    Wei Ren

    2006-01-01

    In the spirit of black hole complementary principle, we have found the noncommutative membrane of Scharzchild black holes. In this paper we extend our results to Kerr black hole and see the same story. Also we make a conjecture that spacetimes are noncommutative on the stretched membrane of the more general Kerr-Newman black hole.

  7. African Journal of Traditional, Complementary and Alternative ...

    African Journals Online (AJOL)

    Differences in attitudes towards/beliefs on complementary and alternative medicine witnessed between physiotherapists, nurses/paramedics and physicians · EMAIL FREE FULL TEXT EMAIL FREE FULL TEXT · DOWNLOAD FULL TEXT DOWNLOAD FULL TEXT. D Živčić, A Racz, D Naletilić, 57-65.

  8. Mental disorders frequency alternative and complementary ...

    African Journals Online (AJOL)

    Objectives: Diabetes mellitus (DM) and hypertension (HT) are chronic disorders with which mental disorders may coexist and for which patients may resort to alternative medicine use. Alternative and complementary medicine is a treatment option that patients tend to use. This study is to determine the prevalence of mental ...

  9. Complementary medicines: When regulation results in revolution

    African Journals Online (AJOL)

    dates, depending on their classification, e.g. antiviral complementary medicines had to be ... must be written in English and at least one other official language and must indicate the ... able task. Furthermore, the cost of merely applying, especially for ... the nature of the industry will change once the new laws are fully.

  10. Comparison of the complementary feeding practices between ...

    African Journals Online (AJOL)

    The aim of this study was to compare the complementary feeding practices between mothers with twins and mothers with singletons. Methods: mother-infant pairs (50 mother-twin pairs and 50 mother-singleton pairs) with children aged 6 to 23 months were recruited from two public health clinics and communities in Tema ...

  11. Complementary Theories to Supply Chain Management

    DEFF Research Database (Denmark)

    Halldorsson, Arni; Hsuan, Juliana; Kotzab, Herbert

    Borrowing from complementary theories has become an important part of theorizing SCM. We build upon principal-agent theory (PAT), transaction cost analysis (TCA), network theory (NT), and resource-based view (RBV) to provide insights on how to structure a supply chain and manage it. Through...

  12. African Journal of Traditional, Complementary and Alternative ...

    African Journals Online (AJOL)

    Anti-diabetic effects of Zhuoduqing formula, a Chinese herbal decoction, ... Bioactive components of Gynura divaricata and its potential use in health, ... Whole-body vibration exercise improves functional parameters in patients ... Survey of dental students' attitude regarding oriental medicine/complementary and alternative ...

  13. Hypertension management: Perspectives of complementary and al ...

    African Journals Online (AJOL)

    Information available on the various forms of Complementary and Alternative Medicine (CAM) used in the management of hypertension is inadequate and conflicting. The primary objective of this study was to assess the use of CAM in the management of hypertension by CAM practition-ers. A qualitative study utilizing ...

  14. (COPD) on complementary and alternative medicine (CAM)

    African Journals Online (AJOL)

    The purpose of this study was to examine the frequency of complementary and alternative medicine usage in Chronic Obstructive Pulmonary Disease (COPD) patients living in the eastern part of Turkey. In this study a descriptive design was used. The study was conducted with 216 patients who were present at the clinic.

  15. African Journal of Traditional, Complementary and Alternative ...

    African Journals Online (AJOL)

    African Journal of Traditional, Complementary and Alternative Medicines. Journal Home · ABOUT THIS JOURNAL · Advanced Search · Current Issue · Archives · Journal Home > Vol 14, No 6 (2017) >. Log in or Register to get access to full text downloads.

  16. Errata | Adewunmi | African Journal of Traditional, Complementary ...

    African Journals Online (AJOL)

    African Journal of Traditional, Complementary and Alternative Medicines. Journal Home · ABOUT THIS JOURNAL · Advanced Search · Current Issue · Archives · Journal Home > Vol 14, No 6 (2017) >. Log in or Register to get access to full text downloads.

  17. Prevalence and Correlates of Complementary and Alternative ...

    African Journals Online (AJOL)

    Background: The rate of complementary and alternative medicine (CAM) use among cancer patients is on the increase worldwide. This is due to the innate urge among humans to try new and alternative ways of medicine, especially where conventional medicine failed to provide satisfactory solution such as in sickle cell ...

  18. Complementary and alternative medicine use among diabetic ...

    African Journals Online (AJOL)

    Abstract. Complementary and alternative medicine (CAM) use is common among patients with chronic diseases in developing countries. The rising use of CAM in the management of diabetes is an emerging public health concern given the potential adverse effects, drug interactions and benefits associated with its use.

  19. African Journal of Traditional, Complementary and Alternative ...

    African Journals Online (AJOL)

    African Journal of Traditional, Complementary and Alternative Medicines. Journal Home · ABOUT THIS JOURNAL · Advanced Search · Current Issue · Archives · Journal Home > Vol 14, No 4S (2017) >. Log in or Register to get access to full text downloads.

  20. Determining Complementary Properties with Quantum Clones

    Science.gov (United States)

    Thekkadath, G. S.; Saaltink, R. Y.; Giner, L.; Lundeen, J. S.

    2017-08-01

    In a classical world, simultaneous measurements of complementary properties (e.g., position and momentum) give a system's state. In quantum mechanics, measurement-induced disturbance is largest for complementary properties and, hence, limits the precision with which such properties can be determined simultaneously. It is tempting to try to sidestep this disturbance by copying the system and measuring each complementary property on a separate copy. However, perfect copying is physically impossible in quantum mechanics. Here, we investigate using the closest quantum analog to this copying strategy, optimal cloning. The coherent portion of the generated clones' state corresponds to "twins" of the input system. Like perfect copies, both twins faithfully reproduce the properties of the input system. Unlike perfect copies, the twins are entangled. As such, a measurement on both twins is equivalent to a simultaneous measurement on the input system. For complementary observables, this joint measurement gives the system's state, just as in the classical case. We demonstrate this experimentally using polarized single photons.

  1. Biodiverse food solutions to enhance complementary feeding

    DEFF Research Database (Denmark)

    Robertson, Aileen; Parlesak, Alexandr; Greiner, Ted

    2016-01-01

    In her recent editorial, Dr. de Pee (2015) states there are two main ways to provide additional nutrients during complementary feeding: fortification and supplementation. She illustrates some problems associated with these ‘solutions’, including lack of compliance. Rather than conclude that lipid...

  2. Optimizing Usability Studies by Complementary Evaluation Methods

    NARCIS (Netherlands)

    Schmettow, Martin; Bach, Cedric; Scapin, Dominique

    2014-01-01

    This paper examines combinations of complementary evaluation methods as a strategy for efficient usability problem discovery. A data set from an earlier study is re-analyzed, involving three evaluation methods applied to two virtual environment applications. Results of a mixed-effects logistic

  3. Transcriptomic responses to darkness stress point to common coral bleaching mechanisms

    Science.gov (United States)

    Desalvo, M. K.; Estrada, A.; Sunagawa, S.; Medina, Mónica

    2012-03-01

    Coral bleaching occurs in response to numerous abiotic stressors, the ecologically most relevant of which is hyperthermic stress due to increasing seawater temperatures. Bleaching events can span large geographic areas and are currently a salient threat to coral reefs worldwide. Much effort has been focused on understanding the molecular and cellular events underlying bleaching, and these studies have mainly utilized heat and light stress regimes. In an effort to determine whether different stressors share common bleaching mechanisms, we used complementary DNA (cDNA) microarrays for the corals Acropora palmata and Montastraea faveolata (containing >10,000 features) to measure differential gene expression during darkness stress. Our results reveal a striking transcriptomic response to darkness in A. palmata involving chaperone and antioxidant up-regulation, growth arrest, and metabolic modifications. As these responses were previously measured during thermal stress, our results suggest that different stressors may share common bleaching mechanisms. Furthermore, our results point to hypoxia and endoplasmic reticulum stress as critical cellular events involved in molecular bleaching mechanisms. On the other hand, we identified a meager transcriptomic response to darkness in M. faveolata where gene expression differences between host colonies and sampling locations were greater than differences between control and stressed fragments. This and previous coral microarray studies reveal the immense range of transcriptomic responses that are possible when studying two coral species that differ greatly in their ecophysiology, thus pointing to the importance of comparative approaches in forecasting how corals will respond to future environmental change.

  4. Rnnotator: an automated de novo transcriptome assembly pipeline from stranded RNA-Seq reads

    Energy Technology Data Exchange (ETDEWEB)

    Martin, Jeffrey; Bruno, Vincent M.; Fang, Zhide; Meng, Xiandong; Blow, Matthew; Zhang, Tao; Sherlock, Gavin; Snyder, Michael; Wang, Zhong

    2010-11-19

    Background: Comprehensive annotation and quantification of transcriptomes are outstanding problems in functional genomics. While high throughput mRNA sequencing (RNA-Seq) has emerged as a powerful tool for addressing these problems, its success is dependent upon the availability and quality of reference genome sequences, thus limiting the organisms to which it can be applied. Results: Here, we describe Rnnotator, an automated software pipeline that generates transcript models by de novo assembly of RNA-Seq data without the need for a reference genome. We have applied the Rnnotator assembly pipeline to two yeast transcriptomes and compared the results to the reference gene catalogs of these organisms. The contigs produced by Rnnotator are highly accurate (95percent) and reconstruct full-length genes for the majority of the existing gene models (54.3percent). Furthermore, our analyses revealed many novel transcribed regions that are absent from well annotated genomes, suggesting Rnnotator serves as a complementary approach to analysis based on a reference genome for comprehensive transcriptomics. Conclusions: These results demonstrate that the Rnnotator pipeline is able to reconstruct full-length transcripts in the absence of a complete reference genome.

  5. Integrative investigation of metabolic and transcriptomic data

    Directory of Open Access Journals (Sweden)

    Önsan Z İlsen

    2006-04-01

    Full Text Available Abstract Background New analysis methods are being developed to integrate data from transcriptome, proteome, interactome, metabolome, and other investigative approaches. At the same time, existing methods are being modified to serve the objectives of systems biology and permit the interpretation of the huge datasets currently being generated by high-throughput methods. Results Transcriptomic and metabolic data from chemostat fermentors were collected with the aim of investigating the relationship between these two data sets. The variation in transcriptome data in response to three physiological or genetic perturbations (medium composition, growth rate, and specific gene deletions was investigated using linear modelling, and open reading-frames (ORFs whose expression changed significantly in response to these perturbations were identified. Assuming that the metabolic profile is a function of the transcriptome profile, expression levels of the different ORFs were used to model the metabolic variables via Partial Least Squares (Projection to Latent Structures – PLS using PLS toolbox in Matlab. Conclusion The experimental design allowed the analyses to discriminate between the effects which the growth medium, dilution rate, and the deletion of specific genes had on the transcriptome and metabolite profiles. Metabolite data were modelled as a function of the transcriptome to determine their congruence. The genes that are involved in central carbon metabolism of yeast cells were found to be the ORFs with the most significant contribution to the model.

  6. Plasma and liver lipidomics response to an intervention of rimonabant in ApoE*3Leiden.CETP transgenic mice.

    Directory of Open Access Journals (Sweden)

    Chunxiu Hu

    Full Text Available Lipids are known to play crucial roles in the development of life-style related risk factors such as obesity, dyslipoproteinemia, hypertension and diabetes. The first selective cannabinoid-1 receptor blocker rimonabant, an anorectic anti-obesity drug, was frequently used in conjunction with diet and exercise for patients with a body mass index greater than 30 kg/m(2 with associated risk factors such as type II diabetes and dyslipidaemia in the past. Less is known about the impact of this drug on the regulation of lipid metabolism in plasma and liver in the early stage of obesity.We designed a four-week parallel controlled intervention on apolipoprotein E3 Leiden cholesteryl ester transfer protein (ApoE*3Leiden.CETP transgenic mice with mild overweight and hypercholesterolemia. A liquid chromatography-linear ion trap-Fourier transform ion cyclotron resonance-mass spectrometric approach was employed to investigate plasma and liver lipid responses to the rimonabant intervention. Rimonabant was found to induce a significant body weight loss (9.4%, p<0.05 and a significant plasma total cholesterol reduction (24%, p<0.05. Six plasma and three liver lipids in ApoE*3Leiden.CETP transgenic mice were detected to most significantly respond to rimonabant treatment. Distinct lipid patterns between the mice were observed for both plasma and liver samples in rimonabant treatment vs. non-treated controls. This study successfully applied, for the first time, systems biology based lipidomics approaches to evaluate treatment effects of rimonabant in the early stage of obesity.The effects of rimonabant on lipid metabolism and body weight reduction in the early stage obesity were shown to be moderate in ApoE*3Leiden.CETP mice on high-fat diet.

  7. Lipidomic approach to identify patterns in phospholipid profiles and define class differences in mammary epithelial and breast cancer cells.

    Science.gov (United States)

    Dória, M Luísa; Cotrim, Zita; Macedo, Bárbara; Simões, Cláudia; Domingues, Pedro; Helguero, Luisa; Domingues, M Rosário

    2012-06-01

    Breast cancer is the leading cause of cancer-related deaths in women. Altered cellular functions of cancer cells lead to uncontrolled cellular growth and morphological changes. Cellular biomembranes are intimately involved in the regulation of cell signaling; however, they remain largely understudied. Phospholipids (PLs) are the main constituents of biological membranes and play important functional, structural and metabolic roles. The aim of this study was to establish if patterns in the PL profiles of mammary epithelial cells and breast cancer cells differ in relation to degree of differentiation and metastatic potential. For this purpose, PLs were analyzed using a lipidomic approach. In brief, PLs were extracted using Bligh and Dyer method, followed by a separation of PL classes by thin layer chromatography, and subsequent analysis by mass spectrometry (MS). Differences and similarities were found in the relative levels of PL content between mammary epithelial and breast cancer cells and between breast cancer cells with different levels of aggressiveness. When compared to the total PL content, phosphatidylcholine levels were reduced and lysophosphatydilcholines increased in the more aggressive cancer cells; while phosphatidylserine levels remained unchanged. MS analysis showed alterations in the classes of phosphatidylcholine, lysophosphatidylcholine, sphingomyelin, and phosphatidylinositides. In particular, the phosphatidylinositides, which are signaling molecules that affect proliferation, survival, and migration, showed dramatic alterations in their profile, where an increase of phosphatdylinositides saturated fatty acids chains and a decrease in C20 fatty acids in cancer cells compared with mammary epithelial cells was observed. At present, information about PL changes in cancer progression is lacking. Therefore, these data will be useful as a starting point to define possible PLs with prospective as biomarkers and disclose metabolic pathways with potential

  8. Pollen lipidomics: lipid profiling exposes a notable diversity in 22 allergenic pollen and potential biomarkers of the allergic immune response.

    Directory of Open Access Journals (Sweden)

    Mohamed Elfatih H Bashir

    Full Text Available BACKGROUND/AIM: Pollen grains are the male gametophytes that deliver sperm cells to female gametophytes during sexual reproduction of higher plants. Pollen is a major source of aeroallergens and environmental antigens. The pollen coat harbors a plethora of lipids that are required for pollen hydration, germination, and penetration of the stigma by pollen tubes. In addition to proteins, pollen displays a wide array of lipids that interact with the human immune system. Prior searches for pollen allergens have focused on the identification of intracellular allergenic proteins, but have largely overlooked much of the extracellular pollen matrix, a region where the majority of lipid molecules reside. Lipid antigens have attracted attention for their potent immunoregulatory effects. By being in close proximity to allergenic proteins on the pollen surface when they interact with host cells, lipids could modify the antigenic properties of proteins. METHODOLOGY/PRINCIPAL FINDINGS: We performed a comparative pollen lipid profiling of 22 commonly allergenic plant species by the use of gas chromatography-mass spectroscopy, followed by detailed data mining and statistical analysis. Three experiments compared pollen lipid profiles. We built a database library of the pollen lipids by matching acquired pollen-lipid mass spectra and retention times with the NIST/EPA/NIH mass-spectral library. We detected, identified, and relatively quantified more than 106 lipid molecular species including fatty acids, n-alkanes, fatty alcohols, and sterols. Pollen-derived lipids stimulation up-regulate cytokines expression of dendritic and natural killer T cells co-culture. CONCLUSIONS/SIGNIFICANCE: Here we report on a lipidomic analysis of pollen lipids that can serve as a database for identifying potential lipid antigens and/or novel candidate molecules involved in allergy. The database provides a resource that facilitates studies on the role of lipids in the

  9. Learning from nature: binary cooperative complementary nanomaterials.

    Science.gov (United States)

    Su, Bin; Guo, Wei; Jiang, Lei

    2015-03-01

    In this Review, nature-inspired binary cooperative complementary nanomaterials (BCCNMs), consisting of two components with entirely opposite physiochemical properties at the nanoscale, are presented as a novel concept for the building of promising materials. Once the distance between the two nanoscopic components is comparable to the characteristic length of some physical interactions, the cooperation between these complementary building blocks becomes dominant and endows the macroscopic materials with novel and superior properties. The first implementation of the BCCNMs is the design of bio-inspired smart materials with superwettability and their reversible switching between different wetting states in response to various kinds of external stimuli. Coincidentally, recent studies on other types of functional nanomaterials contribute more examples to support the idea of BCCNMs, which suggests a potential yet comprehensive range of future applications in both materials science and engineering. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  10. A Diet Rich in Medium-Chain Fatty Acids Improves Systolic Function and Alters the Lipidomic Profile in Patients With Type 2 Diabetes: A Pilot Study.

    Science.gov (United States)

    Airhart, Sophia; Cade, W Todd; Jiang, Hui; Coggan, Andrew R; Racette, Susan B; Korenblat, Kevin; Spearie, Catherine Anderson; Waller, Suzanne; O'Connor, Robert; Bashir, Adil; Ory, Daniel S; Schaffer, Jean E; Novak, Eric; Farmer, Marsha; Waggoner, Alan D; Dávila-Román, Víctor G; Javidan-Nejad, Cylen; Peterson, Linda R

    2016-02-01

    Excessive cardiac long-chain fatty acid (LCFA) metabolism/storage causes cardiomyopathy in animal models of type 2 diabetes. Medium-chain fatty acids (MCFAs) are absorbed and oxidized efficiently. Data in animal models of diabetes suggest MCFAs may benefit the heart. Our objective was to test the effects of an MCFA-rich diet vs an LCFA-rich diet on plasma lipids, cardiac steatosis, and function in patients with type 2 diabetes. This was a double-blind, randomized, 2-week matched-feeding study. The study included ambulatory patients in the general community. Sixteen patients, ages 37-65 years, with type 2 diabetes, an ejection fraction greater than 45%, and no other systemic disease were included. Fourteen days of a diet rich in MCFAs or LCFAs, containing 38% as fat in total, was undertaken. Cardiac steatosis and function were the main outcome measures, with lipidomic changes considered a secondary outcome. The relatively load-independent measure of cardiac contractility, S', improved in the MCFA group (P diet decreased several plasma sphingolipids, ceramide, and acylcarnitines implicated in diabetic cardiomyopathy, and changes in several sphingolipids correlated with improved fasting insulins. Although a diet high in MCFAs does not change cardiac steatosis, our findings suggest that the MCFA-rich diet alters the plasma lipidome and may benefit or at least not harm cardiac function and fasting insulin levels in humans with type 2 diabetes. Larger, long-term studies are needed to further evaluate these effects in less-controlled settings.

  11. A novel approach to the simultaneous extraction and non-targeted analysis of the small molecules metabolome and lipidome using 96-well solid phase extraction plates with column-switching technology.

    Science.gov (United States)

    Li, Yubo; Zhang, Zhenzhu; Liu, Xinyu; Li, Aizhu; Hou, Zhiguo; Wang, Yuming; Zhang, Yanjun

    2015-08-28

    This study combines solid phase extraction (SPE) using 96-well plates with column-switching technology to construct a rapid and high-throughput method for the simultaneous extraction and non-targeted analysis of small molecules metabolome and lipidome based on ultra-performance liquid chromatography quadrupole time-of-flight mass spectrometry. This study first investigated the columns and analytical conditions for small molecules metabolome and lipidome, separated by an HSS T3 and BEH C18 columns, respectively. Next, the loading capacity and actuation duration of SPE were further optimized. Subsequently, SPE and column switching were used together to rapidly and comprehensively analyze the biological samples. The experimental results showed that the new analytical procedure had good precision and maintained sample stability (RSDmetabolome and lipidome to test the throughput. The resulting method represents a new analytical approach for biological samples, and a highly useful tool for researches in metabolomics and lipidomics. Copyright © 2015 Elsevier B.V. All rights reserved.

  12. Complementary methods of transverse emittance measurement

    Energy Technology Data Exchange (ETDEWEB)

    Zagel, James; Hu, Martin; Jansson, Andreas; Thurman-Keup, Randy; Yan, Ming-Jen; /Fermilab

    2008-05-01

    Several complementary transverse emittance monitors have been developed and used at the Fermilab accelerator complex. These include Ionization profile Monitors (IPM), Flying Wires, Schottky detectors and a Synchrotron Light Monitor (Synchlite). Mechanical scrapers have also been used for calibration purposes. This paper describes the various measurement devices by examining their basic features, calibration requirements, systematic uncertainties, and applications to collider operation. A comparison of results from different kinds of measurements is also presented.

  13. ZEROES OF GENERALIZED FRESNEL COMPLEMENTARY INTEGRAL FUNCTIONS

    Directory of Open Access Journals (Sweden)

    Jaime Lobo Segura

    2016-08-01

    Full Text Available Theoretical upper and lower bounds are established for zeroes of a parametric family of functions which are defined by integrals of the same type as the Fresnel complementary integral. Asymptotic properties for these bounds are obtained as well as monotony properties of the localization intervals. Given the value of the parameter an analytical-numerical procedure is deduced to enclose all zeros of a given function with an a priori error.

  14. Reveal quantum correlation in complementary bases

    OpenAIRE

    Shengjun Wu; Zhihao Ma; Zhihua Chen; Sixia Yu

    2014-01-01

    An essential feature of genuine quantum correlation is the simultaneous existence of correlation in complementary bases. We reveal this feature of quantum correlation by defining measures based on invariance under a basis change. For a bipartite quantum state, the classical correlation is the maximal correlation present in a certain optimum basis, while the quantum correlation is characterized as a series of residual correlations in the mutually unbiased bases. Compared with other approaches ...

  15. Plant transcriptomics and responses to environmental stress: an ...

    Indian Academy of Sciences (India)

    3Centre for Environmental Research, Near East University, 33010, Lefkosha, Turkish Republic of the Northern Cyprus. 4Department of ...... Transcriptomic analysis of sense and antisense strands of .... 2008 Stem cell transcriptome profiling via.

  16. Blood transcriptomics: applications in toxicology

    Science.gov (United States)

    Joseph, Pius; Umbright, Christina; Sellamuthu, Rajendran

    2015-01-01

    The number of new chemicals that are being synthesized each year has been steadily increasing. While chemicals are of immense benefit to mankind, many of them have a significant negative impact, primarily owing to their inherent chemistry and toxicity, on the environment as well as human health. In addition to chemical exposures, human exposures to numerous non-chemical toxic agents take place in the environment and workplace. Given that human exposure to toxic agents is often unavoidable and many of these agents are found to have detrimental human health effects, it is important to develop strategies to prevent the adverse health effects associated with toxic exposures. Early detection of adverse health effects as well as a clear understanding of the mechanisms, especially at the molecular level, underlying these effects are key elements in preventing the adverse health effects associated with human exposure to toxic agents. Recent developments in genomics, especially transcriptomics, have prompted investigations into this important area of toxicology. Previous studies conducted in our laboratory and elsewhere have demonstrated the potential application of blood gene expression profiling as a sensitive, mechanistically relevant and practical surrogate approach for the early detection of adverse health effects associated with exposure to toxic agents. The advantages of blood gene expression profiling as a surrogate approach to detect early target organ toxicity and the molecular mechanisms underlying the toxicity are illustrated and discussed using recent studies on hepatotoxicity and pulmonary toxicity. Furthermore, the important challenges this emerging field in toxicology faces are presented in this review article. PMID:23456664

  17. The utility of transcriptomics in fish conservation.

    Science.gov (United States)

    Connon, Richard E; Jeffries, Ken M; Komoroske, Lisa M; Todgham, Anne E; Fangue, Nann A

    2018-01-29

    There is growing recognition of the need to understand the mechanisms underlying organismal resilience (i.e. tolerance, acclimatization) to environmental change to support the conservation management of sensitive and economically important species. Here, we discuss how functional genomics can be used in conservation biology to provide a cellular-level understanding of organismal responses to environmental conditions. In particular, the integration of transcriptomics with physiological and ecological research is increasingly playing an important role in identifying functional physiological thresholds predictive of compensatory responses and detrimental outcomes, transforming the way we can study issues in conservation biology. Notably, with technological advances in RNA sequencing, transcriptome-wide approaches can now be applied to species where no prior genomic sequence information is available to develop species-specific tools and investigate sublethal impacts that can contribute to population declines over generations and undermine prospects for long-term conservation success. Here, we examine the use of transcriptomics as a means of determining organismal responses to environmental stressors and use key study examples of conservation concern in fishes to highlight the added value of transcriptome-wide data to the identification of functional response pathways. Finally, we discuss the gaps between the core science and policy frameworks and how thresholds identified through transcriptomic evaluations provide evidence that can be more readily used by resource managers. © 2018. Published by The Company of Biologists Ltd.

  18. Developmental Transcriptome for a Facultatively Eusocial Bee, Megalopta genalis

    OpenAIRE

    Jones, Beryl M.; Wcislo, William T.; Robinson, Gene E.

    2015-01-01

    Transcriptomes provide excellent foundational resources for mechanistic and evolutionary analyses of complex traits. We present a developmental transcriptome for the facultatively eusocial bee Megalopta genalis, which represents a potential transition point in the evolution of eusociality. A de novo transcriptome assembly of Megalopta genalis was generated using paired-end Illumina sequencing and the Trinity assembler. Males and females of all life stages were aligned to this transcriptome fo...

  19. Young children feeding and Zinc levels of complementary foods in ...

    African Journals Online (AJOL)

    Young children feeding and Zinc levels of complementary foods in Western ... localities helped to identify the recipes used for preparation of complementary foods. ... foods given to them, the cooking methods and the frequency of consumption.

  20. Healing and Preventing Pain: Complementary and Integrative Approaches

    Science.gov (United States)

    ... page please turn JavaScript on. Feature: Pain Management Healing and Preventing Pain, Complementary and Integrative Approaches Past ... Pain Management" Articles Putting A Pause In Pain / Healing and Preventing Pain Complementary and Integrative Approaches / Pain ...

  1. Mind-Body Medicine Practices in Complementary and Alternative Medicine

    Science.gov (United States)

    ... Visitor Information RePORT NIH Fact Sheets Home > Mind-Body Medicine Practices in Complementary and Alternative Medicine Small Text Medium Text Large Text Mind-Body Medicine Practices in Complementary and Alternative Medicine YESTERDAY ...

  2. High Cholesterol and Complementary Health Practices: What the Science Says

    Science.gov (United States)

    ... professionals High Cholesterol and Complementary Health Practices: What the Science Says Share: February 2013 Dietary Supplements Red Yeast ... to exploring complementary health products and practices in the context of rigorous ... health researchers, and disseminating authoritative information ...

  3. Discovering complementary colors from the perspective of steam education

    Science.gov (United States)

    Karabey, Burak; Yigit Koyunkaya, Melike; Enginoglu, Turan; Yurumezoglu, Kemal

    2018-05-01

    This study explored the theory and applications of complementary colors using a technology-based activity designed from the perspective of STEAM education. Complementary colors and their areas of use were examined from the perspective of physics, mathematics and art, respectively. The study, which benefits from technology, makes the theory of complementary colors accessible to all through practical applications and provides a multidisciplinary, integrated and innovative technique of teaching the subject of colors, which could be used to teach complementary colors.

  4. Systematic profiling and comparison of the lipidomes from Panax ginseng, P. quinquefolius, and P. notoginseng by ultrahigh performance supercritical fluid chromatography/high-resolution mass spectrometry and ion mobility-derived collision cross section measurement.

    Science.gov (United States)

    Shi, Xiaojian; Yang, Wenzhi; Qiu, Shi; Hou, Jinjun; Wu, Wanying; Guo, Dean

    2018-05-04

    Lipidomics currently is still confronted with challenges from chromatographic separation and lipids identification. Here we report a lipidomics platform by integrating ultrahigh performance supercritical fluid chromatography/quadrupole time-of-flight mass spectrometry (UHPSFC/QTOF-MS) and collision cross section (CCS) measurement using ion mobility spectroscopy/time-of-flight mass spectrometry (IMS/QTOF-MS), aiming to enhance the profiling performance and identification reliability of lipids. The lipidomes extracted from three congeneric Panax species (P. ginseng, P. quinquefolius, and P. notoginseng) by methyl tert-butyl ether are comprehensively profiled and compared by use of this platform. A potent UHPSFC/QTOF-MS approach was developed on a 1.7-μm particles packed Torus 2-PIC column using CH 3 OH (in CO 2 ) as a modifier and CH 3 OH/0.2 mM ammonium acetate as the makeup liquid, enabling well resolution of six lipid subclasses by both positive and negative MS E modes. In contrast to the reversed-phase chromatography, "normal-phase" like elution order and better resolution of polar lipids and some lipid isomers were achieved by UHPSFC separation. Pattern recognition chemometric analysis of 60 batches of Ginseng samples ultimately unveiled 24 lipid markers, of which triacylglycerols were the most important. Aside from the automated MS database searching against HMDB and LIPID MAPS, the application of CCS retrieval or CCS prediction improved lipid identification by reducing the possible hits. In conclusion, this integral platform can significantly improve the chromatographic separation and the reliability of lipids identification in lipidomics studies. It is the first report that systematically compares the lipidomic difference of three reputable Panax species, providing useful information for their quality control in addition to ginsenoside analysis. Copyright © 2018 Elsevier B.V. All rights reserved.

  5. Metabolomics and transcriptomics identify pathway differences between visceral and subcutaneous adipose tissue in colorectal cancer patients: the ColoCare study.

    Science.gov (United States)

    Liesenfeld, David B; Grapov, Dmitry; Fahrmann, Johannes F; Salou, Mariam; Scherer, Dominique; Toth, Reka; Habermann, Nina; Böhm, Jürgen; Schrotz-King, Petra; Gigic, Biljana; Schneider, Martin; Ulrich, Alexis; Herpel, Esther; Schirmacher, Peter; Fiehn, Oliver; Lampe, Johanna W; Ulrich, Cornelia M

    2015-08-01

    Metabolic and transcriptomic differences between visceral adipose tissue (VAT) and subcutaneous adipose tissue (SAT) compartments, particularly in the context of obesity, may play a role in colorectal carcinogenesis. We investigated the differential functions of their metabolic compositions. Biochemical differences between adipose tissues (VAT compared with SAT) in patients with colorectal carcinoma (CRC) were investigated by using mass spectrometry metabolomics and gene expression profiling. Metabolite compositions were compared between VAT, SAT, and serum metabolites. The relation between patients' tumor stage and metabolic profiles was assessed. Presurgery blood and paired VAT and SAT samples during tumor surgery were obtained from 59 CRC patients (tumor stages I-IV) of the ColoCare cohort. Gas chromatography time-of-flight mass spectrometry and liquid chromatography quadrupole time-of-flight mass spectrometry were used to measure 1065 metabolites in adipose tissue (333 identified compounds) and 1810 metabolites in serum (467 identified compounds). Adipose tissue gene expression was measured by using Illumina's HumanHT-12 Expression BeadChips. Compared with SAT, VAT displayed elevated markers of inflammatory lipid metabolism, free arachidonic acid, phospholipases (PLA2G10), and prostaglandin synthesis-related enzymes (PTGD/PTGS2S). Plasmalogen concentrations were lower in VAT than in SAT, which was supported by lower gene expression of FAR1, the rate-limiting enzyme for ether-lipid synthesis in VAT. Serum sphingomyelin concentrations were inversely correlated (P = 0.0001) with SAT adipose triglycerides. Logistic regression identified lipids in patients' adipose tissues, which were associated with CRC tumor stage. As one of the first studies, we comprehensively assessed differences in metabolic, lipidomic, and transcriptomic profiles between paired human VAT and SAT and their association with CRC tumor stage. We identified markers of inflammation in VAT, which

  6. Complementary feeding practices and nutritional status of children 6 ...

    African Journals Online (AJOL)

    Objectives: Inappropriate complementary feeding practices among children aged 6-23 months is major cause of under nutrition. There is scarce information on the relationship between complementary feeding practices and nutritional status. This study aimed to determine the factors contributing to the complementary ...

  7. Complementary and Alternative Medicine (CAM): Expanding Horizons of Health Care

    Science.gov (United States)

    ... please turn Javascript on. The National Center for Complementary and Alternative Medicine (NCCAM) is this year celebrating 10 years of ... Photo: NCCAM This year, the National Center for Complementary and Alternative Medicine (NCCAM) celebrates its 10th anniversary. We explore complementary ...

  8. Blood transcriptomics and metabolomics for personalized medicine.

    Science.gov (United States)

    Li, Shuzhao; Todor, Andrei; Luo, Ruiyan

    2016-01-01

    Molecular analysis of blood samples is pivotal to clinical diagnosis and has been intensively investigated since the rise of systems biology. Recent developments have opened new opportunities to utilize transcriptomics and metabolomics for personalized and precision medicine. Efforts from human immunology have infused into this area exquisite characterizations of subpopulations of blood cells. It is now possible to infer from blood transcriptomics, with fine accuracy, the contribution of immune activation and of cell subpopulations. In parallel, high-resolution mass spectrometry has brought revolutionary analytical capability, detecting > 10,000 metabolites, together with environmental exposure, dietary intake, microbial activity, and pharmaceutical drugs. Thus, the re-examination of blood chemicals by metabolomics is in order. Transcriptomics and metabolomics can be integrated to provide a more comprehensive understanding of the human biological states. We will review these new data and methods and discuss how they can contribute to personalized medicine.

  9. The Human Transcriptome: An Unfinished Story

    Directory of Open Access Journals (Sweden)

    Mihaela Pertea

    2012-06-01

    Full Text Available Despite recent technological advances, the study of the human transcriptome is still in its early stages. Here we provide an overview of the complex human transcriptomic landscape, present the bioinformatics challenges posed by the vast quantities of transcriptomic data, and discuss some of the studies that have tried to determine how much of the human genome is transcribed. Recent evidence has suggested that more than 90% of the human genome is transcribed into RNA. However, this view has been strongly contested by groups of scientists who argued that many of the observed transcripts are simply the result of transcriptional noise. In this review, we conclude that the full extent of transcription remains an open question that will not be fully addressed until we decipher the complete range and biological diversity of the transcribed genomic sequences.

  10. Complementary and alternative interventions in atopic dermatitis.

    Science.gov (United States)

    Lee, Joohee; Bielory, Leonard

    2010-08-01

    The burden of atopic diseases, including atopic dermatitis (AD), is significant and far-reaching. In addition to cost of care and therapies, it affects the quality of life for those affected as well as their caretakers. Complementary and alternative therapies are commonly used because of concerns about potential adverse effects of conventional therapies and frustration with the lack of response to prescribed medications, be it due to the severity of the AD or the lack of appropriate regular use. Despite the promising results reported with various herbal medicines and biologic products, the clinical efficacy of such alternative therapies remains to be determined. Physicians need to be educated about alternative therapies and discuss benefits and potential adverse effects or limitations with patients. A systematic approach and awareness of reputable and easily accessible resources are helpful in dealing with complementary and alternative medicine (CAM). The use of CAM interventions is common among individuals with AD. Epidemiologic data have been a motivating drive for better elucidation of the efficacy of CAM interventions for allergic disease. Herbal medicines and biologics for AD treatment and, more recently, prevention comprise a major area of clinical investigation. Potential mechanisms of therapeutic effect elucidated by animal models and human clinical studies implicate modulation of TH2-type allergic inflammation and induction of immune tolerance. Population-based research regarding the use of CAM for allergic diseases underscores the increasing challenge for care providers with respect to identifying CAM use and ensuring safe use of allopathic and complementary medicines in disease management. Copyright 2010. Published by Elsevier Inc.

  11. Complementary arsenic speciation methods: A review

    Energy Technology Data Exchange (ETDEWEB)

    Nearing, Michelle M., E-mail: michelle.nearing@rmc.ca; Koch, Iris, E-mail: koch-i@rmc.ca; Reimer, Kenneth J., E-mail: reimer-k@rmc.ca

    2014-09-01

    The toxicity of arsenic greatly depends on its chemical form and oxidation state (speciation) and therefore accurate determination of arsenic speciation is a crucial step in understanding its chemistry and potential risk. High performance liquid chromatography with inductively coupled mass spectrometry (HPLC–ICP-MS) is the most common analysis used for arsenic speciation but it has two major limitations: it relies on an extraction step (usually from a solid sample) that can be incomplete or alter the arsenic compounds; and it provides no structural information, relying on matching sample peaks to standard peaks. The use of additional analytical methods in a complementary manner introduces the ability to address these disadvantages. The use of X-ray absorption spectroscopy (XAS) with HPLC–ICP-MS can be used to identify compounds not extracted for HPLC–ICP-MS and provide minimal processing steps for solid state analysis that may help preserve labile compounds such as those containing arsenic-sulfur bonds, which can degrade under chromatographic conditions. On the other hand, HPLC–ICP-MS is essential in confirming organoarsenic compounds with similar white line energies seen by using XAS, and identifying trace arsenic compounds that are too low to be detected by XAS. The complementary use of electrospray mass spectrometry (ESI–MS) with HPLC–ICP-MS provides confirmation of arsenic compounds identified during the HPLC–ICP-MS analysis, identification of unknown compounds observed during the HPLC–ICP-MS analysis and further resolves HPLC–ICP-MS by identifying co-eluting compounds. In the complementary use of HPLC–ICP-MS and ESI–MS, HPLC–ICP-MS helps to focus the ESI–MS selection of ions. Numerous studies have shown that the information obtained from HPLC–ICP-MS analysis can be greatly enhanced by complementary approaches. - Highlights: • HPLC–ICP-MS is the most common method used for arsenic speciation. • HPLC limitations include

  12. Complementary alternative medicine and nuclear medicine

    International Nuclear Information System (INIS)

    Werneke, Ursula; McCready, V.Ralph

    2004-01-01

    Complementary alternative medicines (CAMs), including food supplements, are taken widely by patients, especially those with cancer. Others take CAMs hoping to improve fitness or prevent disease. Physicians (and patients) may not be aware of the potential side-effects and interactions of CAMs with conventional treatment. Likewise, their known physiological effects could interfere with radiopharmaceutical kinetics, producing abnormal treatment responses and diagnostic results. Nuclear medicine physicians are encouraged to question patients on their intake of CAMs when taking their history prior to radionuclide therapy or diagnosis. The potential effect of CAMs should be considered when unexpected therapeutic or diagnostic results are found. (orig.)

  13. Complementary Theories to Supply Chain Management Revisited

    DEFF Research Database (Denmark)

    Halldorsson, Arni; Hsuan, Juliana; Kotzab, Herbert

    2015-01-01

    Purpose – The aim of this paper is to identify ways by which the theorizing of supply chain management (SCM) takes place, with particular attention to complementary theories. SCM suffers as well as benefits from a “conceptual slack”. Design/methodology/approach – The nature of SCM is discussed...... as organizational units that act or consummate an action that delivers a particular performance. Originality/value – This paper portrays SCM sensitivity to managerial challenges by moving from borrowing to a more bilateral view on theorizing of SCM, reflecting the nature of SCM....

  14. The Perils of Complementary Alternative Medicine

    Directory of Open Access Journals (Sweden)

    Michael J. Bayme

    2014-07-01

    Full Text Available More than 11,000 articles lauding alternative medicine appear in the PubMed database, but there are only a few articles describing the complications of such care. Two patients suffering from complications of alternative medicine were treated in our hospital: one patient developed necrotizing fasciitis after acupuncture, and the second developed an epidural hematoma after chiropractic manipulation. These complications serve as a clarion call to the Israeli Health Ministry, as well as to health ministries around the world, to include complementary medicine under its inspection and legislative authority.

  15. Complementary arsenic speciation methods: A review

    International Nuclear Information System (INIS)

    Nearing, Michelle M.; Koch, Iris; Reimer, Kenneth J.

    2014-01-01

    The toxicity of arsenic greatly depends on its chemical form and oxidation state (speciation) and therefore accurate determination of arsenic speciation is a crucial step in understanding its chemistry and potential risk. High performance liquid chromatography with inductively coupled mass spectrometry (HPLC–ICP-MS) is the most common analysis used for arsenic speciation but it has two major limitations: it relies on an extraction step (usually from a solid sample) that can be incomplete or alter the arsenic compounds; and it provides no structural information, relying on matching sample peaks to standard peaks. The use of additional analytical methods in a complementary manner introduces the ability to address these disadvantages. The use of X-ray absorption spectroscopy (XAS) with HPLC–ICP-MS can be used to identify compounds not extracted for HPLC–ICP-MS and provide minimal processing steps for solid state analysis that may help preserve labile compounds such as those containing arsenic-sulfur bonds, which can degrade under chromatographic conditions. On the other hand, HPLC–ICP-MS is essential in confirming organoarsenic compounds with similar white line energies seen by using XAS, and identifying trace arsenic compounds that are too low to be detected by XAS. The complementary use of electrospray mass spectrometry (ESI–MS) with HPLC–ICP-MS provides confirmation of arsenic compounds identified during the HPLC–ICP-MS analysis, identification of unknown compounds observed during the HPLC–ICP-MS analysis and further resolves HPLC–ICP-MS by identifying co-eluting compounds. In the complementary use of HPLC–ICP-MS and ESI–MS, HPLC–ICP-MS helps to focus the ESI–MS selection of ions. Numerous studies have shown that the information obtained from HPLC–ICP-MS analysis can be greatly enhanced by complementary approaches. - Highlights: • HPLC–ICP-MS is the most common method used for arsenic speciation. • HPLC limitations include

  16. Explicit MDS Codes with Complementary Duals

    DEFF Research Database (Denmark)

    Beelen, Duals Peter; Jin, Lingfei

    2018-01-01

    In 1964, Massey introduced a class of codes with complementary duals which are called Linear Complimentary Dual (LCD for short) codes. He showed that LCD codes have applications in communication system, side-channel attack (SCA) and so on. LCD codes have been extensively studied in literature....... On the other hand, MDS codes form an optimal family of classical codes which have wide applications in both theory and practice. The main purpose of this paper is to give an explicit construction of several classes of LCD MDS codes, using tools from algebraic function fields. We exemplify this construction...

  17. Complementary and Alternative Therapies in ALS

    Science.gov (United States)

    Bedlack, Richard S.; Joyce, Nanette; Carter, Gregory T.; Pagononi, Sabrina; Karam, Chafic

    2015-01-01

    Synopsis Given the severity of their illness and lack of effective disease modifying agents, it is not surprising that most patients with ALS consider trying complementary and alternative therapies. Some of the most commonly considered alternative therapies include special diets, nutritional supplements, cannabis, acupuncture, chelation and energy healing. This chapter reviews these in detail. We also describe 3 models by which physicians may frame discussions about alternative therapies: paternalism, autonomy and shared decision making. Finally, we review a program called ALSUntangled which using shared shared decision making to review alternative therapies for ALS. PMID:26515629

  18. Complementary and alternative medicine in pulmonology.

    Science.gov (United States)

    Mark, John D; Chung, Youngran

    2015-06-01

    To provide a comprehensive review of complementary and alternative medicine (CAM) therapies for the treatment of pulmonary disorders in children. The use of complementary medicine (CAM) is commonly used by both children and adults with breathing problems, and especially in chronic pulmonary disorders such as asthma and cystic fibrosis. Many clinics and hospitals now offer CAM, even though most of the conventionally trained health practitioners have little knowledge or education regarding CAM therapies. Research in CAM that demonstrates overall benefit is lacking, especially in children. Often parents do not report CAM use to their child's healthcare provider and this could compromise their overall quality of care. Although many research studies evaluating CAM therapies have methodological flaws, data exist to support CAM therapies in treating children with pulmonary disorders. This review examines the latest evidence of CAM use and effectiveness in children with pulmonary disorders. Physicians should be aware of the many CAM therapy options and the research surrounding them in order to provide their patients with the most current and accurate information available.

  19. Complementary and Alternative Medicine and Osteoarthritis.

    Science.gov (United States)

    Wang, Chenchen

    2013-01-01

    Patients with osteoarthritis experience high levels of pain, psychological distress and have limited therapeutic options. Emerging evidence from clinical trials suggests that both acupuncture and Tai Chi mind-body therapies are safe and effective treatments for osteoarthritis. Acupuncture has effects over and above those of 'sham acupuncture' and the most robust evidence to date demonstrates that acupuncture does have short-term benefits and is a reasonable referral option for patients with symptomatic osteoarthritis. Tai Chi is a mind-body exercise that enhances cardiovascular fitness, muscular strength, balance, and physical function. It also appears to be associated with reduced stress and anxiety and depression, as well as improved quality of life. Thus, Tai Chi may be safely recommended to patients with osteoarthritis as a complementary and alternative medical approach to affect patient well-being. Integrative approaches combine the best of conventional medicine and complementary and alternative medicine to ultimately improve patient care. These modalities may lead to the development of better disease modifying strategies that could improve symptoms and decrease the progression of osteoarthritis. This overview synthesizes the current body of knowledge about Chinese mind-body medicine to better inform clinical decision-making for our rheumatic patients.

  20. The transcriptome of Toxoplasma gondii

    Directory of Open Access Journals (Sweden)

    Roos David S

    2005-12-01

    Full Text Available Abstract Background Toxoplasma gondii gives rise to toxoplasmosis, among the most prevalent parasitic diseases of animals and man. Transformation of the tachzyoite stage into the latent bradyzoite-cyst form underlies chronic disease and leads to a lifetime risk of recrudescence in individuals whose immune system becomes compromised. Given the importance of tissue cyst formation, there has been intensive focus on the development of methods to study bradyzoite differentiation, although the molecular basis for the developmental switch is still largely unknown. Results We have used serial analysis of gene expression (SAGE to define the Toxoplasma gondii transcriptome of the intermediate-host life cycle that leads to the formation of the bradyzoite/tissue cyst. A broad view of gene expression is provided by >4-fold coverage from nine distinct libraries (~300,000 SAGE tags representing key developmental transitions in primary parasite populations and in laboratory strains representing the three canonical genotypes. SAGE tags, and their corresponding mRNAs, were analyzed with respect to abundance, uniqueness, and antisense/sense polarity and chromosome distribution and developmental specificity. Conclusion This study demonstrates that phenotypic transitions during parasite development were marked by unique stage-specific mRNAs that accounted for 18% of the total SAGE tags and varied from 1–5% of the tags in each developmental stage. We have also found that Toxoplasma mRNA pools have a unique parasite-specific composition with 1 in 5 transcripts encoding Apicomplexa-specific genes functioning in parasite invasion and transmission. Developmentally co-regulated genes were dispersed across all Toxoplasma chromosomes, as were tags representing each abundance class, and a variety of biochemical pathways indicating that trans-acting mechanisms likely control gene expression in this parasite. We observed distinct similarities in the specificity and

  1. Scrimer: designing primers from transcriptome data

    Czech Academy of Sciences Publication Activity Database

    Mořkovský, Libor; Pačes, Jan; Rídl, Jakub; Reifová, R.

    2015-01-01

    Roč. 15, č. 6 (2015), s. 1415-1420 ISSN 1755-098X R&D Projects: GA MŠk EE2.3.20.0303 Institutional support: RVO:68081766 ; RVO:68378050 Keywords : next-generation sequencing * primer design * SNaPshot * SNP genotyping * transcriptome Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 5.298, year: 2015

  2. Global daily dynamics of the pineal transcriptome

    DEFF Research Database (Denmark)

    Bustos, Diego M; Bailey, Michael J; Sugden, David

    2011-01-01

    Transcriptome profiling of the pineal gland has revealed night/day differences in the expression of a major fraction of the genes active in this tissue, with two-thirds of these being nocturnal increases. A set of over 600 transcripts exhibit two-fold to >100-fold daily differences in abundance...

  3. The transcriptome landscape of early maize meiosis

    Science.gov (United States)

    Meiosis, particularly meiotic recombination, is a major factor affecting yield and breeding of plants. To gain insight into the transcriptome landscape during early initiation steps of meiotic recombination, we profiled early prophase I meiocytes from maize using RNA-seq. Our analyses of genes prefe...

  4. The renal transcriptome in experimental hypertension

    NARCIS (Netherlands)

    Wesseling, S.

    2007-01-01

    The renal transcriptome in experimental hypertension The kidneys importantly determine blood pressure. Kidney dysfunction can result in hypertension, which in turn leads to renal damage. In primary hypertension the cause is unknown. The condition is polygenic, however, which genetic defects cause

  5. Transcriptome analysis of Anopheles stephensi embryo using ...

    Indian Academy of Sciences (India)

    Germ band retraction (GBR) stage is one of the important stages during insect development. It is associated with an extensive epithelial morphogenesis and may also be pivotal in generation of morphological diversity in insects. Despite its importance, only a handful of studies report the transcriptome repertoire of this stage ...

  6. Brain transcriptome atlases : A computational perspective

    NARCIS (Netherlands)

    Mahfouz, A.M.E.T.A.; Huisman, S.M.H.; Lelieveldt, B.P.F.; Reinders, M.J.T.

    2017-01-01

    The immense complexity of the mammalian brain is largely reflected in the underlying molecular signatures of its billions of cells. Brain transcriptome atlases provide valuable insights into gene expression patterns across different brain areas throughout the course of development. Such atlases

  7. Applications of Fourier Transform Ion Cyclotron Resonance (FT-ICR) and Orbitrap Based High Resolution Mass Spectrometry in Metabolomics and Lipidomics

    Science.gov (United States)

    Ghaste, Manoj; Mistrik, Robert; Shulaev, Vladimir

    2016-01-01

    Metabolomics, along with other “omics” approaches, is rapidly becoming one of the major approaches aimed at understanding the organization and dynamics of metabolic networks. Mass spectrometry is often a technique of choice for metabolomics studies due to its high sensitivity, reproducibility and wide dynamic range. High resolution mass spectrometry (HRMS) is a widely practiced technique in analytical and bioanalytical sciences. It offers exceptionally high resolution and the highest degree of structural confirmation. Many metabolomics studies have been conducted using HRMS over the past decade. In this review, we will explore the latest developments in Fourier transform mass spectrometry (FTMS) and Orbitrap based metabolomics technology, its advantages and drawbacks for using in metabolomics and lipidomics studies, and development of novel approaches for processing HRMS data. PMID:27231903

  8. Lipidomics: the function of vital lipids in embryogenesis preventing autism spectrum disorders, treating sterile inflammatory diatheses with a lymphopoietic central nervous system component.

    Science.gov (United States)

    Tallberg, Thomas; Dabek, Jan; Hallamaa, Raija; Atroshi, Faik

    2011-01-01

    The central role performed by billions of vital central nervous system (CNS) lipids "lipidomics" in medical physiology is usually overlooked. A metabolic deficiency embracing these vital lipids can form the aetiology for a variety of diseases. CNS lipids regulate embryogenesis, cell induction, mental balance by preventing autism spectrum disorders, depression, burn-out syndromes like posttraumatic stress disease PTSD, by guarding normal immunity, treating sterile inflammatory diatheses with a titanium containing lymphopoietic CNS lipid component. The propaganda driving for unphysiological fat-free diets is dangerous and can cause serious health problems for a whole generation. This article presents a broad list of various mental and motor bodily functions of which the healthy function depends on these vital CNS lipids. A rigorous fat-free diet can provoke these metabolic lipid deficiencies but they can fortunately be compensated by dietary supplementation, but not by pharmacologic treatment.

  9. Characterization and discrimination of Taihe black-boned silky fowl (Gallus gallus domesticus Brisson) muscles using LC/MS-based lipidomics.

    Science.gov (United States)

    Mi, Si; Shang, Ke; Jia, Wei; Zhang, Chun-Hui; Li, Xia; Fan, Yu-Qing; Wang, Hang

    2018-07-01

    Taihe black-boned silky fowl (Gallus gallus domesticus Brisson) has a history of over 2200 years of being consumed as a curative food in China. In this work, an LC/MS-based lipidomics approach was employed to investigate the characteristic lipid composition of Taihe black-boned silky fowls from different ages and genders as well as from different carcass parts. Data were processed using an orthogonal partial least squares discriminant analysis and one-way analysis of variance. A total of 1127 lipids were detected in Taihe black-boned silky fowl muscles. Among them, 88, 11 and 1 lipid species were found to have both a variable influence on a projection value >1 and a p-value smaller than 0.05 between different age, gender and part groups. These results illustrate that the influence of the 3 investigated factors on the lipid profiles of Taihe black-boned silky fowl decreased in the order of age > gender > part. Lipid profile differences will facilitate a better understanding of the curative properties of Taihe black-boned silky fowl. Taihe and crossbred black-boned silky fowls were compared in terms of their lipid compositions based on the same strategy. The results showed that the two groups were able to discriminate from each other effectively. 47 lipid compounds were determined to be potential markers for the authentication of Taihe black-boned silky fowl. This work demonstrates the successful application of lipidomics for lipid profiling in food raw materials. Copyright © 2018 Elsevier Ltd. All rights reserved.

  10. Top-down and bottom-up lipidomic analysis of rabbit lipoproteins under different metabolic conditions using flow field-flow fractionation, nanoflow liquid chromatography and mass spectrometry.

    Science.gov (United States)

    Byeon, Seul Kee; Kim, Jin Yong; Lee, Ju Yong; Chung, Bong Chul; Seo, Hong Seog; Moon, Myeong Hee

    2015-07-31

    This study demonstrated the performances of top-down and bottom-up approaches in lipidomic analysis of lipoproteins from rabbits raised under different metabolic conditions: healthy controls, carrageenan-induced inflammation, dehydration, high cholesterol (HC) diet, and highest cholesterol diet with inflammation (HCI). In the bottom-up approach, the high density lipoproteins (HDL) and the low density lipoproteins (LDL) were size-sorted and collected on a semi-preparative scale using a multiplexed hollow fiber flow field-flow fractionation (MxHF5), followed by nanoflow liquid chromatography-ESI-MS/MS (nLC-ESI-MS/MS) analysis of the lipids extracted from each lipoprotein fraction. In the top-down method, size-fractionated lipoproteins were directly infused to MS for quantitative analysis of targeted lipids using chip-type asymmetrical flow field-flow fractionation-electrospray ionization-tandem mass spectrometry (cAF4-ESI-MS/MS) in selected reaction monitoring (SRM) mode. The comprehensive bottom-up analysis yielded 122 and 104 lipids from HDL and LDL, respectively. Rabbits within the HC and HCI groups had lipid patterns that contrasted most substantially from those of controls, suggesting that HC diet significantly alters the lipid composition of lipoproteins. Among the identified lipids, 20 lipid species that exhibited large differences (>10-fold) were selected as targets for the top-down quantitative analysis in order to compare the results with those from the bottom-up method. Statistical comparison of the results from the two methods revealed that the results were not significantly different for most of the selected species, except for those species with only small differences in concentration between groups. The current study demonstrated that top-down lipid analysis using cAF4-ESI-MS/MS is a powerful high-speed analytical platform for targeted lipidomic analysis that does not require the extraction of lipids from blood samples. Copyright © 2015 Elsevier B

  11. Abrasive water jet: a complementary tool

    International Nuclear Information System (INIS)

    Duarte, J.P.; Pecas, P.; Nunes, E.; Gouveia, H.

    1998-01-01

    The abrasive water jet is a powerful cutting tool, whose main advantages lie in the absence of thermal effects and the capability of cutting highly thick materials. Compared with Laser, the abrasive water jet allows the cutting of a larger range of thicknesses and a wider variety of materials such as: ornamental stones, metals, polymers, composites, wood, glass ceramics. The application of this technology has suffered and extensive growth, with successful applications in varied industrial sectors like the automotive, aerospace, textile, metalworking, ornamental stones, etc. The present communication aims at introducing the abrasive water jet as a complementary tool to laser cutting, presenting its advantages by showing some documented examples of pieces cut for different industries. (Author) 5 refs

  12. Complementary and alternative treatment of musculoskeletal pain.

    Science.gov (United States)

    Grazio, Simeon; Balen, Diana

    2011-12-01

    The use of complementary and alternative medicine (CAM) is high and increasing worldwide. Patients usually use CAM in addition to conventional medicine, mainly to treat pain. In a large number of cases, people use CAM for chronic musculoskeletal pain as in osteoarthritis, back pain, neck pain, or fibromyalgia. Herewith, a review is presented of CAM efficacy in treating musculoskeletal pain for which, however, no scientific research has so far provided evidence solid enough. In some rare cases where adequate pain control cannot be achieved, CAM might be considered in rational and individual approach based on the first general rule in medicine "not to harm" and on the utility theory of each intervention, i.e. according to the presumed mechanism of painful stimulus and with close monitoring of the patient's response. Further high quality studies are warranted to elucidate the efficacy and side effects of CAM methods. Therefore, conventional medicine remains the main mode of treatment for patients with musculoskeletal painful conditions.

  13. Western and Eastern Values are Complementary

    Directory of Open Access Journals (Sweden)

    Ashok Natarajan

    2018-05-01

    Full Text Available All values are spiritual in their essence, even those that appear to be physical. For all values seek perfection of the whole. The widest and highest perfection is based on the totality and oneness of reality. Such a perfection is comprehensive and inclusive. It is founded on truths that complete other truths rather than compete with them. Despite their vast cultural differences, Eastern and Western values reflect complementary aspects of a unified whole. But the process of developing values in any society depends on its underlying cultural perspective. The nature of mind is such that it divides and analyzes reality, and concentrates on one thing at a time, whereas spirituality is founded on the perception of the whole. This vast difference in underlying cultural orientation helps explain the immense gulf in understanding that has long distinguished and separated the cultures of Asia and Europe.

  14. Transcriptome-wide analysis supports environmental adaptations of two Pinus pinaster populations from contrasting habitats.

    Science.gov (United States)

    Cañas, Rafael A; Feito, Isabel; Fuente-Maqueda, José Francisco; Ávila, Concepción; Majada, Juan; Cánovas, Francisco M

    2015-11-06

    Maritime pine (Pinus pinaster Aiton) grows in a range of different climates in the southwestern Mediterranean region and the existence of a variety of latitudinal ecotypes or provenances is well established. In this study, we have conducted a deep analysis of the transcriptome in needles from two P. pinaster provenances, Leiria (Portugal) and Tamrabta (Morocco), which were grown in northern Spain under the same conditions. An oligonucleotide microarray (PINARRAY3) and RNA-Seq were used for whole-transcriptome analyses, and we found that 90.95% of the data were concordant between the two platforms. Furthermore, the two methods identified very similar percentages of differentially expressed genes with values of 5.5% for PINARRAY3 and 5.7% for RNA-Seq. In total, 6,023 transcripts were shared and 88 differentially expressed genes overlapped in the two platforms. Among the differentially expressed genes, all transport related genes except aquaporins were expressed at higher levels in Tamrabta than in Leiria. In contrast, genes involved in secondary metabolism were expressed at higher levels in Tamrabta, and photosynthesis-related genes were expressed more highly in Leiria. The genes involved in light sensing in plants were well represented in the differentially expressed groups of genes. In addition, increased levels of hormones such as abscisic acid, gibberellins, jasmonic and salicylic acid were observed in Leiria. Both transcriptome platforms have proven to be useful resources, showing complementary and reliable results. The results presented here highlight the different abilities of the two maritime pine populations to sense environmental conditions and reveal one type of regulation that can be ascribed to different genetic and epigenetic backgrounds.

  15. Transcriptomic and proteomic analysis of Oenococcus oeni adaptation to wine stress conditions

    Directory of Open Access Journals (Sweden)

    Mar Margalef-Català

    2016-09-01

    Full Text Available Oenococcus oeni, the main lactic acid bacteria responsible for malolactic fermentation in wine, has to adapt to stressful conditions, such as low pH and high ethanol content. In this study, the changes in the transcriptome and the proteome of O. oeni PSU-1 during the adaptation period before MLF start have been studied. DNA microarrays were used for the transcriptomic analysis and two complementary proteomic techniques, 2-D DIGE and iTRAQ labeling were used to analyze the proteomic response. One of the most influenced functions in PSU-1 due to inoculation into wine-like medium (WLM was translation, showing the over-expression of certain ribosomal genes and the corresponding proteins. Amino acid metabolism and transport was also altered and several peptidases were up regulated both at gene and protein level. Certain proteins involved in glutamine and glutamate metabolism showed an increased abundance revealing the key role of nitrogen uptake under stressful conditions. A strong transcriptional inhibition of carbohydrate metabolism related genes was observed. On the other hand, the transcriptional up-regulation of malate transport and citrate consumption was indicative of the use of L-malate and citrate associated to stress response and as an alternative energy source to sugar metabolism. Regarding the stress mechanisms, our results support the relevance of the thioredoxin and glutathione systems in the adaptation of O. oeni to wine related stress. Genes and proteins related to cell wall showed also significant changes indicating the relevance of the cell envelop as protective barrier to environmental stress. The differences found between transcriptomic and proteomic data suggested the relevance of post-transcriptional mechanisms and the complexity of the stress response in O. oeni adaptation. Further research should deepen into the metabolisms mostly altered due to wine conditions to elucidate the role of each mechanism in the O. oeni ability to

  16. An emerging picture of the seed desiccome: confirmed regulators and newcomers identified using transcriptome comparison.

    Science.gov (United States)

    Terrasson, Emmanuel; Buitink, Julia; Righetti, Karima; Ly Vu, Benoit; Pelletier, Sandra; Zinsmeister, Julia; Lalanne, David; Leprince, Olivier

    2013-01-01

    Desiccation tolerance (DT) is the capacity to withstand total loss of cellular water. It is acquired during seed filling and lost just after germination. However, in many species, a germinated seed can regain DT under adverse conditions such as osmotic stress. The genes, proteins and metabolites that are required to establish this DT is referred to as the desiccome. It includes both a range of protective mechanisms and underlying regulatory pathways that remain poorly understood. As a first step toward the identification of the seed desiccome of Medicago truncatula, using updated microarrays we characterized the overlapping transcriptomes associated with acquisition of DT in developing seeds and the re-establishment of DT in germinated seeds using a polyethylene glycol treatment (-1.7 MPa). The resulting list contained 740 and 2829 transcripts whose levels, respectively, increased and decreased with DT. Fourty-eight transcription factors (TF) were identified including MtABI3, MtABI5 and many genes regulating flowering transition and cell identity. A promoter enrichment analysis revealed a strong over-representation of ABRE elements together with light-responsive cis-acting elements. In Mtabi5 Tnt1 insertion mutants, DT could no longer be re-established by an osmotic stress. Transcriptome analysis on Mtabi5 radicles during osmotic stress revealed that 13 and 15% of the up-regulated and down-regulated genes, respectively, are mis-regulated in the mutants and might be putative downstream targets of MtABI5 implicated in the re-establishment of DT. Likewise, transcriptome comparisons of the desiccation sensitive Mtabi3 mutants and hairy roots ectopically expressing MtABI3 revealed that 35 and 23% of the up-regulated and down-regulated genes are acting downstream of MtABI3. Our data suggest that ABI3 and ABI5 have complementary roles in DT. Whether DT evolved by co-opting existing pathways regulating flowering and cellular phase transition and cell identity is discussed.

  17. The initiation of complementary feeding among Qom indigenous people

    OpenAIRE

    Irene Olmedo, Sofía; Valeggia, Claudia

    2014-01-01

    As of six months of life, breastfeeding no longer covers an infant’s energy or micronutrient needs, so appropriate complementary feeding should be provided. The objective of this study was to assess the time and adequacy for introducing complementary feeding in a Qom/Toba population and analyze the sociocultural concepts of families regarding complementary feeding. Quantitative and qualitative data were collected by participant observation and semistructured surveys administered to mothers of...

  18. Detection of G-Quadruplex Structures Formed by G-Rich Sequences from Rice Genome and Transcriptome Using Combined Probes.

    Science.gov (United States)

    Chang, Tianjun; Li, Weiguo; Ding, Zhan; Cheng, Shaofei; Liang, Kun; Liu, Xiangjun; Bing, Tao; Shangguan, Dihua

    2017-08-01

    Putative G-quadruplex (G4) forming sequences (PQS) are highly prevalent in the genome and transcriptome of various organisms and are considered as potential regulation elements in many biological processes by forming G4 structures. The formation of G4 structures highly depends on the sequences and the environment. In most cases, it is difficult to predict G4 formation by PQS, especially PQS containing G2 tracts. Therefore, the experimental identification of G4 formation is essential in the study of G4-related biological functions. Herein, we report a rapid and simple method for the detection of G4 structures by using a pair of complementary reporters, hemin and BMSP. This method was applied to detect G4 structures formed by PQS (DNA and RNA) searched in the genome and transcriptome of Oryza sativa. Unlike most of the reported G4 probes that only recognize part of G4 structures, the proposed method based on combined probes positively responded to almost all G4 conformations, including parallel, antiparallel, and mixed/hybrid G4, but did not respond to non-G4 sequences. This method shows potential for high-throughput identification of G4 structures in genome and transcriptome. Furthermore, BMSP was observed to drive some PQS to form more stable G4 structures or induce the G4 formation of some PQS that cannot form G4 in normal physiological conditions, which may provide a powerful molecular tool for gene regulation.

  19. The transcriptomic changes associated with the development of social parasitism in the honeybee Apis mellifera capensis

    Science.gov (United States)

    Aumer, Denise; Mumoki, Fiona N.; Pirk, Christian W. W.; Moritz, Robin F. A.

    2018-04-01

    Social insects are characterized by the division of labor. Queens usually dominate reproduction, whereas workers fulfill non-reproductive age-dependent tasks to maintain the colony. Although workers are typically sterile, they can activate their ovaries to produce their own offspring. In the extreme, worker reproduction can turn into social parasitism as in Apis mellifera capensis. These intraspecific parasites occupy a host colony, kill the resident queen, and take over the reproductive monopoly. Because they exhibit a queenlike behavior and are also treated like queens by the fellow workers, they are so-called pseudoqueens. Here, we compare the development of parasitic pseudoqueens and social workers at different time points using fat body transcriptome data. Two complementary analysis methods—a principal component analysis and a time course analysis—led to the identification of a core set of genes involved in the transition from a social worker into a highly fecund parasitic pseudoqueen. Comparing our results on pseudoqueens with gene expression data of honeybee queens revealed many similarities. In addition, there was a set of specific transcriptomic changes in the parasitic pseudoqueens that differed from both, queens and social workers, which may be typical for the development of the social parasitism in A. m. capensis.

  20. Developmental Transcriptomic Features of the Carcinogenic Liver Fluke, Clonorchis sinensis

    Science.gov (United States)

    Cho, Pyo Yun; Kim, Tae Im; Cho, Shin-Hyeong; Choi, Sang-Haeng; Park, Hong-Seog; Kim, Tong-Soo; Hong, Sung-Jong

    2011-01-01

    Clonorchis sinensis is the causative agent of the life-threatening disease endemic to China, Korea, and Vietnam. It is estimated that about 15 million people are infected with this fluke. C. sinensis provokes inflammation, epithelial hyperplasia, and periductal fibrosis in bile ducts, and may cause cholangiocarcinoma in chronically infected individuals. Accumulation of a large amount of biological information about the adult stage of this liver fluke in recent years has advanced our understanding of the pathological interplay between this parasite and its hosts. However, no developmental gene expression profiles of C. sinensis have been published. In this study, we generated gene expression profiles of three developmental stages of C. sinensis by analyzing expressed sequence tags (ESTs). Complementary DNA libraries were constructed from the adult, metacercaria, and egg developmental stages of C. sinensis. A total of 52,745 ESTs were generated and assembled into 12,830 C. sinensis assembled EST sequences, and then these assemblies were further categorized into groups according to biological functions and developmental stages. Most of the genes that were differentially expressed in the different stages were consistent with the biological and physical features of the particular developmental stage; high energy metabolism, motility and reproduction genes were differentially expressed in adults, minimal metabolism and final host adaptation genes were differentially expressed in metacercariae, and embryonic genes were differentially expressed in eggs. The higher expression of glucose transporters, proteases, and antioxidant enzymes in the adults accounts for active uptake of nutrients and defense against host immune attacks. The types of ion channels present in C. sinensis are consistent with its parasitic nature and phylogenetic placement in the tree of life. We anticipate that the transcriptomic information on essential regulators of development, bile chemotaxis, and

  1. Developmental transcriptomic features of the carcinogenic liver fluke, Clonorchis sinensis.

    Directory of Open Access Journals (Sweden)

    Won Gi Yoo

    2011-06-01

    Full Text Available Clonorchis sinensis is the causative agent of the life-threatening disease endemic to China, Korea, and Vietnam. It is estimated that about 15 million people are infected with this fluke. C. sinensis provokes inflammation, epithelial hyperplasia, and periductal fibrosis in bile ducts, and may cause cholangiocarcinoma in chronically infected individuals. Accumulation of a large amount of biological information about the adult stage of this liver fluke in recent years has advanced our understanding of the pathological interplay between this parasite and its hosts. However, no developmental gene expression profiles of C. sinensis have been published. In this study, we generated gene expression profiles of three developmental stages of C. sinensis by analyzing expressed sequence tags (ESTs. Complementary DNA libraries were constructed from the adult, metacercaria, and egg developmental stages of C. sinensis. A total of 52,745 ESTs were generated and assembled into 12,830 C. sinensis assembled EST sequences, and then these assemblies were further categorized into groups according to biological functions and developmental stages. Most of the genes that were differentially expressed in the different stages were consistent with the biological and physical features of the particular developmental stage; high energy metabolism, motility and reproduction genes were differentially expressed in adults, minimal metabolism and final host adaptation genes were differentially expressed in metacercariae, and embryonic genes were differentially expressed in eggs. The higher expression of glucose transporters, proteases, and antioxidant enzymes in the adults accounts for active uptake of nutrients and defense against host immune attacks. The types of ion channels present in C. sinensis are consistent with its parasitic nature and phylogenetic placement in the tree of life. We anticipate that the transcriptomic information on essential regulators of development

  2. Global meta-analysis of transcriptomics studies.

    Directory of Open Access Journals (Sweden)

    José Caldas

    Full Text Available Transcriptomics meta-analysis aims at re-using existing data to derive novel biological hypotheses, and is motivated by the public availability of a large number of independent studies. Current methods are based on breaking down studies into multiple comparisons between phenotypes (e.g. disease vs. healthy, based on the studies' experimental designs, followed by computing the overlap between the resulting differential expression signatures. While useful, in this methodology each study yields multiple independent phenotype comparisons, and connections are established not between studies, but rather between subsets of the studies corresponding to phenotype comparisons. We propose a rank-based statistical meta-analysis framework that establishes global connections between transcriptomics studies without breaking down studies into sets of phenotype comparisons. By using a rank product method, our framework extracts global features from each study, corresponding to genes that are consistently among the most expressed or differentially expressed genes in that study. Those features are then statistically modelled via a term-frequency inverse-document frequency (TF-IDF model, which is then used for connecting studies. Our framework is fast and parameter-free; when applied to large collections of Homo sapiens and Streptococcus pneumoniae transcriptomics studies, it performs better than similarity-based approaches in retrieving related studies, using a Medical Subject Headings gold standard. Finally, we highlight via case studies how the framework can be used to derive novel biological hypotheses regarding related studies and the genes that drive those connections. Our proposed statistical framework shows that it is possible to perform a meta-analysis of transcriptomics studies with arbitrary experimental designs by deriving global expression features rather than decomposing studies into multiple phenotype comparisons.

  3. Transcriptome architecture across tissues in the pig

    Directory of Open Access Journals (Sweden)

    Folch Josep M

    2008-04-01

    Full Text Available Abstract Background Artificial selection has resulted in animal breeds with extreme phenotypes. As an organism is made up of many different tissues and organs, each with its own genetic programme, it is pertinent to ask: How relevant is tissue in terms of total transcriptome variability? Which are the genes most distinctly expressed between tissues? Does breed or sex equally affect the transcriptome across tissues? Results In order to gain insight on these issues, we conducted microarray expression profiling of 16 different tissues from four animals of two extreme pig breeds, Large White and Iberian, two males and two females. Mixed model analysis and neighbor – joining trees showed that tissues with similar developmental origin clustered closer than those with different embryonic origins. Often a sound biological interpretation was possible for overrepresented gene ontology categories within differentially expressed genes between groups of tissues. For instance, an excess of nervous system or muscle development genes were found among tissues of ectoderm or mesoderm origins, respectively. Tissue accounted for ~11 times more variability than sex or breed. Nevertheless, we were able to confidently identify genes with differential expression across tissues between breeds (33 genes and between sexes (19 genes. The genes primarily affected by sex were overall different than those affected by breed or tissue. Interaction with tissue can be important for differentially expressed genes between breeds but not so much for genes whose expression differ between sexes. Conclusion Embryonic development leaves an enduring footprint on the transcriptome. The interaction in gene × tissue for differentially expressed genes between breeds suggests that animal breeding has targeted differentially each tissue's transcriptome.

  4. Comparative Analysis of the Arabidopsis Pollen Transcriptome

    Czech Academy of Sciences Publication Activity Database

    Honys, David; Twell, D.

    2003-01-01

    Roč. 132, - (2003), s. 640ů652 ISSN 0032-0889 R&D Projects: GA AV ČR IAA5038207 Grant - others:Royal Society(GB) NATO Postdoctoral Fellowship (to D.H.) Institutional research plan: CEZ:AV0Z5038910; CEZ:MSM 113100003 Keywords : transcriptome profiling * Arabidopsis pollen * male gametophyte Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 5.634, year: 2003

  5. Transcriptome Dynamics during Maize Endosperm Development.

    Directory of Open Access Journals (Sweden)

    Jianzhou Qu

    Full Text Available The endosperm is a major organ of the seed that plays vital roles in determining seed weight and quality. However, genome-wide transcriptome patterns throughout maize endosperm development have not been comprehensively investigated to date. Accordingly, we performed a high-throughput RNA sequencing (RNA-seq analysis of the maize endosperm transcriptome at 5, 10, 15 and 20 days after pollination (DAP. We found that more than 11,000 protein-coding genes underwent alternative splicing (AS events during the four developmental stages studied. These genes were mainly involved in intracellular protein transport, signal transmission, cellular carbohydrate metabolism, cellular lipid metabolism, lipid biosynthesis, protein modification, histone modification, cellular amino acid metabolism, and DNA repair. Additionally, 7,633 genes, including 473 transcription factors (TFs, were differentially expressed among the four developmental stages. The differentially expressed TFs were from 50 families, including the bZIP, WRKY, GeBP and ARF families. Further analysis of the stage-specific TFs showed that binding, nucleus and ligand-dependent nuclear receptor activities might be important at 5 DAP, that immune responses, signalling, binding and lumen development are involved at 10 DAP, that protein metabolic processes and the cytoplasm might be important at 15 DAP, and that the responses to various stimuli are different at 20 DAP compared with the other developmental stages. This RNA-seq analysis provides novel, comprehensive insights into the transcriptome dynamics during early endosperm development in maize.

  6. Transposable elements in the Anopheles funestus transcriptome.

    Science.gov (United States)

    Fernández-Medina, Rita D; Carareto, Claudia M A; Struchiner, Cláudio J; Ribeiro, José M C

    2017-06-01

    Transposable elements (TEs) are present in most of the eukaryotic genomes and their impact on genome evolution is increasingly recognized. Although there is extensive information on the TEs present in several eukaryotic genomes, less is known about the expression of these elements at the transcriptome level. Here we present a detailed analysis regarding the expression of TEs in Anopheles funestus, the second most important vector of human malaria in Africa. Several transcriptionally active TE families belonging both to Class I and II were identified and characterized. Interestingly, we have identified a full-length putative active element (including the presence of full length TIRs in the genomic sequence) belonging to the hAT superfamily, which presents active members in other insect genomes. This work contributes to a comprehensive understanding of the landscape of transposable elements in A. funestus transcriptome. Our results reveal that TEs are abundant and diverse in the mosquito and that most of the TE families found in the genome are represented in the mosquito transcriptome, a fact that could indicate activity of these elements.The vast diversity of TEs expressed in A. funestus suggests that there is ongoing amplification of several families in this organism.

  7. Fusing complementary images for pavement cracking measurements

    International Nuclear Information System (INIS)

    Yao, Ming; Zhao, Zuyun; Xu, Bugao; Yao, Xun

    2015-01-01

    Cracking is a major pavement distress that jeopardizes road serviceability and traffic safety. Automated pavement distress survey (APDS) systems have been developed using digital imaging technology to replace human surveys for more timely and accurate inspections. Most APDS systems require special lighting devices to illuminate pavements and prevent shadows of roadside objects that distort cracks in the image. Most artificial lighting devices are laser based, and are either hazardous to unprotected people or require dedicated power supplies on the vehicle. This study was aimed to develop a new imaging system that can scan pavement surface at highway speed and determine the level of severity of pavement cracking without using any artificial lighting. The new system consists of dual line-scan cameras that are installed side by side to scan the same pavement area as the vehicle moves. Cameras are controlled with different exposure settings so that both sunlit and shadowed areas can be visible in two separate images. The paired images contain complementary details useful for reconstructing an image in which the shadows are eliminated. This paper intends to present (1) the design of the dual line-scan camera system, (2) a new calibration method for line-scan cameras to rectify and register paired images, (3) a customized image-fusion algorithm that merges the multi-exposure images into one shadow-free image for crack detection, and (4) the results of the field tests on a selected road over a long period. (paper)

  8. Cerebral asymmetries: complementary and independent processes.

    Directory of Open Access Journals (Sweden)

    Gjurgjica Badzakova-Trajkov

    Full Text Available Most people are right-handed and left-cerebrally dominant for speech, leading historically to the general notion of left-hemispheric dominance, and more recently to genetic models proposing a single lateralizing gene. This hypothetical gene can account for higher incidence of right-handers in those with left cerebral dominance for speech. It remains unclear how this dominance relates to the right-cerebral dominance for some nonverbal functions such as spatial or emotional processing. Here we use functional magnetic resonance imaging with a sample of 155 subjects to measure asymmetrical activation induced by speech production in the frontal lobes, by face processing in the temporal lobes, and by spatial processing in the parietal lobes. Left-frontal, right-temporal, and right-parietal dominance were all intercorrelated, suggesting that right-cerebral biases may be at least in part complementary to the left-hemispheric dominance for language. However, handedness and parietal asymmetry for spatial processing were uncorrelated, implying independent lateralizing processes, one producing a leftward bias most closely associated with handedness, and the other a rightward bias most closely associated with spatial attention.

  9. Alternative and complementary medicine in cancer patient

    International Nuclear Information System (INIS)

    Reckova, M.

    2009-01-01

    The use of alternative and complementary medicine (CAM) in cancer patients is widespread and it is not surprising as the results gained by conventional treatments are not sufficient. However, the results from the studies with CAM are not always sufficient according to their testing in appropriate clinical studies. Another problem that is present in the use of CAM is the possibility of drug-drug interactions between conventional therapies and CAM. Thus, it is of utmost importance that the oncologist possess a good knowledge of available CAM and provide a sufficient time for discussion with the patient and his/her family about possible alternative treatments and any downside risks. The cornerstone for pertinent discussion is sufficient knowledge on the part of the oncologist about those alternative treatments that are usually presented in the media with incomplete information about their relevant clinical tests and side effects. The following article presents a review of the current alternative treatment methods with a focus on the alternative drugs that have already been clinically tested, and secondarily on the alternative drugs that have been used even without sufficient testing in clinical trials. (author)

  10. Pet birds II. Complementary diagnostic procedures

    International Nuclear Information System (INIS)

    Beregi, A.; Molnar, V.; Felkai, F.; Biro, F.

    1997-01-01

    Microscopical examinations are useful in detecting bacteria from droppings and body fluids. Antimicrobial susceptibility tests are also used to perform antimicrobial therapy. Parasitological examinations can also be done on pet birds. Hematological examinations are not very common because of the difficulties in determining the normal serum values that might vary by species and sexes. The vena cutanea ulnaris is the best vein for drawing blood from a pet bird but nail clipping for this purpose is also widely used. The most common and basic complementary examination method is radiology. Birds can be radiographed without anesthesia. Ventrodorsal and latero-lateral pictures are required. The right positioning and setting the adequate values is the most important. Contrast radiographs can also be made on birds. Endoscopy is widely used for sex determination but also can be used for the examination of abdominal organs. Ultrasound examination of pet birds is not a common method because of the difficulties provided by the air sacs. ECG is not a widely used method either because of the high heart beat frequency of birds. Other methods such as necropsy, cytological, histological and toxicological examinations can also be performed on pet birds

  11. Complementary technologies for verification of excess plutonium

    International Nuclear Information System (INIS)

    Langner, D.G.; Nicholas, N.J.; Ensslin, N.; Fearey, B.L.; Mitchell, D.J.; Marlow, K.W.; Luke, S.J.; Gosnell, T.B.

    1998-01-01

    Three complementary measurement technologies have been identified as candidates for use in the verification of excess plutonium of weapons origin. These technologies: high-resolution gamma-ray spectroscopy, neutron multiplicity counting, and low-resolution gamma-ray spectroscopy, are mature, robust technologies. The high-resolution gamma-ray system, Pu-600, uses the 630--670 keV region of the emitted gamma-ray spectrum to determine the ratio of 240 Pu to 239 Pu. It is useful in verifying the presence of plutonium and the presence of weapons-grade plutonium. Neutron multiplicity counting is well suited for verifying that the plutonium is of a safeguardable quantity and is weapons-quality material, as opposed to residue or waste. In addition, multiplicity counting can independently verify the presence of plutonium by virtue of a measured neutron self-multiplication and can detect the presence of non-plutonium neutron sources. The low-resolution gamma-ray spectroscopic technique is a template method that can provide continuity of knowledge that an item that enters the a verification regime remains under the regime. In the initial verification of an item, multiple regions of the measured low-resolution spectrum form a unique, gamma-radiation-based template for the item that can be used for comparison in subsequent verifications. In this paper the authors discuss these technologies as they relate to the different attributes that could be used in a verification regime

  12. Complementary, alternative, integrative, or unconventional medicine?

    Science.gov (United States)

    Penson, R T; Castro, C M; Seiden, M V; Chabner, B A; Lynch, T J

    2001-01-01

    Shortly before his death in 1995, Kenneth B. Schwartz, a cancer patient at Massachusetts General Hospital (MGH), founded the Kenneth B. Schwartz Center. The Schwartz Center is a non-profit organization dedicated to supporting and advancing compassionate health care delivery, which provides hope to the patient, support to caregivers, and sustenance to the healing process. The center sponsors the Schwartz Center Rounds, a monthly multidisciplinary forum where caregivers reflect on important psychosocial issues faced by patients, their families, and their caregivers, and gain insight and support from fellow staff members. Interest in complementary and alternative medicine (CAM) has grown exponentially in the past decade, fueled by Internet marketing, dissatisfaction with mainstream medicine, and a desire for patients to be actively involved in their health care. There is a large discordance between physician estimates and reported prevalence of CAM use. Many patients do not disclose their practices mainly because they believe CAM falls outside the rubric of conventional medicine or because physicians do not ask. Concern about drug interactions and adverse effects are compounded by a lack of Food and Drug Administration regulation. Physicians need to be informed about CAM and be attuned to the psychosocial needs of patients.

  13. Behavior analysis and neuroscience: Complementary disciplines.

    Science.gov (United States)

    Donahoe, John W

    2017-05-01

    Behavior analysis and neuroscience are disciplines in their own right but are united in that both are subfields of a common overarching field-biology. What most fundamentally unites these disciplines is a shared commitment to selectionism, the Darwinian mode of explanation. In selectionism, the order and complexity observed in nature are seen as the cumulative products of selection processes acting over time on a population of variants-favoring some and disfavoring others-with the affected variants contributing to the population on which future selections operate. In the case of behavior analysis, the central selection process is selection by reinforcement; in neuroscience it is natural selection. The two selection processes are inter-related in that selection by reinforcement is itself the product of natural selection. The present paper illustrates the complementary nature of behavior analysis and neuroscience through considering their joint contributions to three central problem areas: reinforcement-including conditioned reinforcement, stimulus control-including equivalence classes, and memory-including reminding and remembering. © 2017 Society for the Experimental Analysis of Behavior.

  14. Use of Complementary and Alternative Medicine for Work Related ...

    African Journals Online (AJOL)

    Conclusion: Complementary and alternative medicine therapies may improve quality of life, reduce work disruptions and enhance job satisfaction for dentists who suffer from work-related musculoskeletal disorders. It is important that dentists incorporate complementary and alternative medicine strategies into practice to ...

  15. Discovering Complementary Colors from the Perspective of STEAM Education

    Science.gov (United States)

    Karabey, Burak; Koyunkaya, Melike Yigit; Enginoglu, Turan; Yurumezoglu, Kemal

    2018-01-01

    This study explored the theory and applications of complementary colors using a technology-based activity designed from the perspective of STEAM education. Complementary colors and their areas of use were examined from the perspective of physics, mathematics and art, respectively. The study, which benefits from technology, makes the theory of…

  16. Complementary feeding: a commentary by the ESPGHAN Committee on Nutrition

    NARCIS (Netherlands)

    Agostoni, Carlo; Decsi, Tamas; Fewtrell, Mary; Goulet, Olivier; Kolacek, Sanja; Koletzko, Berthold; Michaelsen, Kim Fleischer; Moreno, Luis; Puntis, John; Rigo, Jacques; Shamir, Raanan; Szajewska, Hania; Turck, Dominique; van Goudoever, Johannes

    2008-01-01

    This position paper on complementary feeding summarizes evidence for health effects of complementary foods. It focuses on healthy infants in Europe. After reviewing current knowledge and practices, we have formulated these conclusions: Exclusive or full breast-feeding for about 6 months is a

  17. Complementary Therapies – a spiritual resource in recovery-processes?

    DEFF Research Database (Denmark)

    Lunde, Anita; Dürr, Dorte Wiwe; Johannessen, Helle

    rehabilitative treatments intends to support recovery processes of people with serious mental illness. Aim: To investigate how employees and residents perceive complementary therapies as an integral rehabilitative treatment, and to explore the recovery related implications of spirituality employed in the use...... and health as well as for the ethics of providing complementary treatment practice in social psychiatry....

  18. Special Section: Complementary and Alternative Medicine (CAM): Time to Talk

    Science.gov (United States)

    ... to discuss with your health care providers any complementary and alternative medicines you take or are thinking about starting. Photo: ... adults 50 and older use some form of complementary and alternative medicine (CAM). But less than one-third who use ...

  19. Adoption of Enriched Local Complementary Food in Osun State ...

    African Journals Online (AJOL)

    Locally processed complementary foods, appropriately enriched can complement breast milk and traditional foods during the nutritionally vulnerable periods of a child life. The study therefore examines the adoption of enriched local complementary foods in Osun State Nigeria. Structured interview schedule was used to ...

  20. Reconfigurable Complementary Logic Circuits with Ambipolar Organic Transistors.

    Science.gov (United States)

    Yoo, Hocheon; Ghittorelli, Matteo; Smits, Edsger C P; Gelinck, Gerwin H; Lee, Han-Koo; Torricelli, Fabrizio; Kim, Jae-Joon

    2016-10-20

    Ambipolar organic electronics offer great potential for simple and low-cost fabrication of complementary logic circuits on large-area and mechanically flexible substrates. Ambipolar transistors are ideal candidates for the simple and low-cost development of complementary logic circuits since they can operate as n-type and p-type transistors. Nevertheless, the experimental demonstration of ambipolar organic complementary circuits is limited to inverters. The control of the transistor polarity is crucial for proper circuit operation. Novel gating techniques enable to control the transistor polarity but result in dramatically reduced performances. Here we show high-performance non-planar ambipolar organic transistors with electrical control of the polarity and orders of magnitude higher performances with respect to state-of-art split-gate ambipolar transistors. Electrically reconfigurable complementary logic gates based on ambipolar organic transistors are experimentally demonstrated, thus opening up new opportunities for ambipolar organic complementary electronics.

  1. Use of complementary and alternative medicines during the third trimester.

    Science.gov (United States)

    Pallivalapila, Abdul Rouf; Stewart, Derek; Shetty, Ashalatha; Pande, Binita; Singh, Rajvir; McLay, James S

    2015-01-01

    To estimate the prevalence, indications, and associated factors for complementary and alternative medicine use during the last trimester of pregnancy. A questionnaire survey was conducted of women with a live birth (N=700) admitted to the postnatal unit at the Royal Aberdeen Maternity Hospital, northeast Scotland. Outcome measures included: complementary and alternative medicine used; vitamins and minerals used; reasons for complementary and alternative medicine use; independent associated factors for use; views; and experiences. Descriptive and inferential statistical analysis was performed. The response rate was 79.6% of eligible women. Two thirds of respondents (61.4%) reported using complementary and alternative medicine, excluding vitamins and minerals, during the third trimester. Respondents reported using a total of 30 different complementary and alternative medicine modalities, of which oral herbal products were the most common (38% of respondents, 40 different products). The independent associated factors for complementary and alternative medicine use identified were: complementary and alternative medicine use before pregnancy (odds ratio [OR] 4.36, 95% confidence interval [CI] 2.39-7.95, Palternative medicine use by family or friends (OR 2.36, 95% CI 1.61-3.47, Palternative medicines were safer than prescribed medicines (P=.006), less likely to be associated with side effects (P≤.001), and could interfere with conventional medicines (P≤.001). Despite the majority of respondents, and notably users, being uncertain about their safety and effectiveness, complementary and alternative medicine modalities and complementary and alternative medicine products are widely used during the third trimester of pregnancy in this study population. Although prior use was the most significant independent associated factor, the role of family and friends, rather than health professionals, in the decision to use complementary and alternative medicine may be of concern

  2. [The situation of complementary medicine in Germany].

    Science.gov (United States)

    Albrecht, Henning

    2013-01-01

    With the amendment of the German Medicinal Products Act in 1976 and the inclusion of naturopathy and homeopathy into the German Medical Licensure Act from 1988, the German government set up a comparatively favorable framework for Complementary and Alternative Medicine (CAM). But no comprehensive integration into the academic operating systems followed, because the universities as well as the legislative body seemed to have no further interest in CAM. Therefore, research projects in the field and suitable professorships had and still have to be financed by third-party funds. Notwithstanding the success of several CAM-projects, no sustainable development could be established: When the third-party funding runs off and the protagonists retire the institutional structures are supposed to vanish as well. Although the public demand for CAM is high in Germany, the administration detached homeopathy as a compulsory subject from the German Medical Licensure Act in 2002 and restricted severely the refunding of naturopathic medicines by the statutory health insurance in 2004. Moreover, the trend for CAM bashing takes root in the media. Unfortunately the CAM scene does not close ranks and is incapable to implement fundamental data collection processes into daily clinical routine: A wide range of data could justify further efforts to the government as well as to the scientific community. To say something positive, it must be mentioned that the scientific standard of CAM research is high for the most part and that third-party funded projects deliver remarkable results ever and on. Copyright © 2013 S. Karger AG, Basel.

  3. Complementary Therapies and Medicines and Reproductive Medicine.

    Science.gov (United States)

    Smith, Caroline A; Armour, Mike; Ee, Carolyn

    2016-03-01

    Complementary therapies and medicines are a broad and diverse range of treatments, and are frequently used by women and their partners during the preconception period to assist with infertility, and to address pregnancy-related conditions. Despite frequent use, the evidence examining the efficacy, effectiveness, and safety for many modalities is lacking, with variable study quality. In this article, we provide an overview of research evidence with the aim of examining the evidence to inform clinical practice. During the preconception period, there is mixed evidence for acupuncture to improve ovulation, or increase pregnancy rates. Acupuncture may improve sperm quality, but there is insufficient evidence to determine whether this results in improved pregnancy and live birth rates. Acupuncture can be described as a low-risk intervention. Chinese and Western herbal medicines may increase pregnancy rates; however, study quality is low. The evaluation of efficacy, effectiveness, and safety during the first trimester of pregnancy has most commonly reported on herbs, supplements, and practices such as acupuncture. There is high-quality evidence reporting the benefits of herbal medicines and acupuncture to treat nausea in pregnancy. The benefit from ginger to manage symptoms of nausea in early pregnancy is incorporated in national clinical guidelines, and vitamin B6 is recommended as a first-line treatment for nausea and vomiting in pregnancy. The safety of ginger and vitamin B6 is considered to be well established, and is based on epidemiological studies. Acupuncture has been shown to reduce back pain and improve function for women in early pregnancy. There is little evidence to support the use of cranberries in pregnancy for prevention of urinary tract infections, and chiropractic treatment for back pain. Overall the numbers of studies are small and of low quality, although the modalities appear to be low risk of harm. Thieme Medical Publishers 333 Seventh Avenue, New

  4. Abrasive water jet: a complementary tool

    Directory of Open Access Journals (Sweden)

    Duarte, J. P.

    1998-04-01

    Full Text Available The abrasive water jet is a powerful cutting tool, whose main advantages lie in the absence of thermal effects and the capability of cutting highly thick materials. Compared with Laser, the abrasive water jet allows the cutting of a larger range of thicknesses and a wider variety of materials such as: ornamental stones, metals, polymers, composites, wood, glass and ceramics. The application of this technology has suffered an extensive growth, with successful applications in varied industrial sectors like the automotive, aerospace, textile, metalworking, ornamental stones, etc. The present communication aims at introducing the abrasive water jet as a complementary tool to laser cutting, presenting its advantages by showing some documented examples of pieces cut for different industries.

    O jacto de água abrasivo é uma poderosa ferramenta de corte, tendo como principais vantagens a ausência de processo térmico e permitir o corte de elevadas espessuras. Comparativamente com o laser o jacto de água abrasivo permite cortar uma maior gama de espessuras, e uma maior diversidade de materiais: rochas ornamentais, metais, polimeros, compósitos, madeiras, vidro e cerâmicos. A aplicação desta tecnologia tem sofrido um crescimento acentuado, existindo aplicações de sucesso nos mais variados sectores industriáis como a indústria automóvel, aeroespacial, têxtil, metalomecânica e rochas ornamentáis. Esta comunição pretende apresentar o corte por jacto de agua abrasivo como uma ferramenta de corte complementar ao corte por laser, apresentando as suas vantagens documentadas através de alguns exemplos de peças executadas para as diferentes indústrias.

  5. Restored in vivo-like membrane lipidomics positively influence in vitro features of cultured mesenchymal stromal/stem cells derived from human placenta.

    Science.gov (United States)

    Chatgilialoglu, Alexandros; Rossi, Martina; Alviano, Francesco; Poggi, Paola; Zannini, Chiara; Marchionni, Cosetta; Ricci, Francesca; Tazzari, Pier Luigi; Taglioli, Valentina; Calder, Philip C; Bonsi, Laura

    2017-02-07

    The study of lipid metabolism in stem cell physiology has recently raised great interest. The role of lipids goes beyond the mere structural involvement in assembling extra- and intra-cellular compartments. Nevertheless, we are still far from understanding the impact of membrane lipidomics in stemness maintenance and differentiation patterns. In the last years, it has been reported how in vitro cell culturing can modify membrane lipidomics. The aim of the present work was to study the membrane fatty acid profile of mesenchymal stromal cells (MSCs) derived from human fetal membranes (hFM-MSCs) and to correlate this to specific biological properties by using chemically defined tailored lipid supplements (Refeed®). Freshly isolated hFM-MSCs were characterized for their membrane fatty acid composition. hFM-MSCs were cultivated in vitro following a classical protocol and their membrane fatty acid profile at different passages was compared to the profile in vivo. A tailored Refeed® lipid supplement was developed with the aim of reducing the differences created by the in vitro cultivation and was tested on cultured hFM-MSCs. Cell morphology, viability, proliferation, angiogenic differentiation, and immunomodulatory properties after in vitro exposure to the tailored Refeed® lipid supplement were investigated. A significant modification of hFM-MSC membrane fatty acid composition occurred during in vitro culture. Using a tailored lipid supplement, the fatty acid composition of cultured cells remained more similar to their in vivo counterparts, being characterized by a higher polyunsaturated and omega-6 fatty acid content. These changes in membrane composition had no effect on cell morphology and viability, but were linked with increased cell proliferation rate, angiogenic differentiation, and immunomodulatory properties. In particular, Refeed®-supplemented hFM-MSCs showed greater ability to express fully functional cell membrane molecules. Culturing hFM-MSCs alters their

  6. Transcriptome complexity in a genome-reduced bacterium

    DEFF Research Database (Denmark)

    Güell, Marc; van Noort, Vera; Yus, Eva

    2009-01-01

    To study basic principles of transcriptome organization in bacteria, we analyzed one of the smallest self-replicating organisms, Mycoplasma pneumoniae. We combined strand-specific tiling arrays, complemented by transcriptome sequencing, with more than 252 spotted arrays. We detected 117 previousl...

  7. The Escherichia coli transcriptome linked to growth fitness

    Directory of Open Access Journals (Sweden)

    Bei-Wen Ying

    2016-03-01

    Full Text Available A series of Escherichia coli strains with varied genomic sequences were subjected to high-density microarray analyses to elucidate the fitness-correlated transcriptomes. Fitness, which is commonly evaluated by the growth rate during the exponential phase, is not only determined by the genome but is also linked to growth conditions, e.g., temperature. We previously reported genetic and environmental contributions to E. coli transcriptomes and evolutionary transcriptome changes in thermal adaptation. Here, we describe experimental details on how to prepare microarray samples that truly represent the growth fitness of the E. coli cells. A step-by-step record of sample preparation procedures that correspond to growing cells and transcriptome data sets that are deposited at the GEO database (GSE33212, GSE52770, GSE61739 are also provided for reference. Keywords: Transcriptome, Growth fitness, Escherichia coli, Microarray

  8. Transcriptome sequencing and comparative transcriptome analysis of the scleroglucan producer Sclerotium rolfsii

    Directory of Open Access Journals (Sweden)

    Stahl Ulf

    2010-05-01

    Full Text Available Abstract Background The plant pathogenic basidiomycete Sclerotium rolfsii produces the industrially exploited exopolysaccharide scleroglucan, a polymer that consists of (1 → 3-β-linked glucose with a (1 → 6-β-glycosyl branch on every third unit. Although the physicochemical properties of scleroglucan are well understood, almost nothing is known about the genetics of scleroglucan biosynthesis. Similarly, the biosynthetic pathway of oxalate, the main by-product during scleroglucan production, has not been elucidated yet. In order to provide a basis for genetic and metabolic engineering approaches, we studied scleroglucan and oxalate biosynthesis in S. rolfsii using different transcriptomic approaches. Results Two S. rolfsii transcriptomes obtained from scleroglucan-producing and scleroglucan-nonproducing conditions were pooled and sequenced using the 454 pyrosequencing technique yielding ~350,000 reads. These could be assembled into 21,937 contigs and 171,833 singletons, for which 6,951 had significant matches in public protein data bases. Sequence data were used to obtain first insights into the genomics of scleroglucan and oxalate production and to predict putative proteins involved in the synthesis of both metabolites. Using comparative transcriptomics, namely Agilent microarray hybridization and suppression subtractive hybridization, we identified ~800 unigenes which are differently expressed under scleroglucan-producing and non-producing conditions. From these, candidate genes were identified which could represent potential leads for targeted modification of the S. rolfsii metabolism for increased scleroglucan yields. Conclusions The results presented in this paper provide for the first time genomic and transcriptomic data about S. rolfsii and demonstrate the power and usefulness of combined transcriptome sequencing and comparative microarray analysis. The data obtained allowed us to predict the biosynthetic pathways of scleroglucan and

  9. Transcriptomic dissection of tongue squamous cell carcinoma

    Directory of Open Access Journals (Sweden)

    Schwartz Joel L

    2008-02-01

    Full Text Available Abstract Background The head and neck/oral squamous cell carcinoma (HNOSCC is a diverse group of cancers, which develop from many different anatomic sites and are associated with different risk factors and genetic characteristics. The oral tongue squamous cell carcinoma (OTSCC is one of the most common types of HNOSCC. It is significantly more aggressive than other forms of HNOSCC, in terms of local invasion and spread. In this study, we aim to identify specific transcriptomic signatures that associated with OTSCC. Results Genome-wide transcriptomic profiles were obtained for 53 primary OTSCCs and 22 matching normal tissues. Genes that exhibit statistically significant differences in expression between OTSCCs and normal were identified. These include up-regulated genes (MMP1, MMP10, MMP3, MMP12, PTHLH, INHBA, LAMC2, IL8, KRT17, COL1A2, IFI6, ISG15, PLAU, GREM1, MMP9, IFI44, CXCL1, and down-regulated genes (KRT4, MAL, CRNN, SCEL, CRISP3, SPINK5, CLCA4, ADH1B, P11, TGM3, RHCG, PPP1R3C, CEACAM7, HPGD, CFD, ABCA8, CLU, CYP3A5. The expressional difference of IL8 and MMP9 were further validated by real-time quantitative RT-PCR and immunohistochemistry. The Gene Ontology analysis suggested a number of altered biological processes in OTSCCs, including enhancements in phosphate transport, collagen catabolism, I-kappaB kinase/NF-kappaB signaling cascade, extracellular matrix organization and biogenesis, chemotaxis, as well as suppressions of superoxide release, hydrogen peroxide metabolism, cellular response to hydrogen peroxide, keratinization, and keratinocyte differentiation in OTSCCs. Conclusion In summary, our study provided a transcriptomic signature for OTSCC that may lead to a diagnosis or screen tool and provide the foundation for further functional validation of these specific candidate genes for OTSCC.

  10. Moral injury: A new challenge for complementary and alternative medicine.

    Science.gov (United States)

    Kopacz, Marek S; Connery, April L; Bishop, Todd M; Bryan, Craig J; Drescher, Kent D; Currier, Joseph M; Pigeon, Wilfred R

    2016-02-01

    Moral injury represents an emerging clinical construct recognized as a source of morbidity in current and former military personnel. Finding effective ways to support those affected by moral injury remains a challenge for both biomedical and complementary and alternative medicine. This paper introduces the concept of moral injury and suggests two complementary and alternative medicine, pastoral care and mindfulness, which may prove useful in supporting military personnel thought to be dealing with moral injury. Research strategies for developing an evidence-base for applying these, and other, complementary and alternative medicine modalities to moral injury are discussed. Published by Elsevier Ltd.

  11. Realization of a complementary medium using dielectric photonic crystals.

    Science.gov (United States)

    Xu, Tao; Fang, Anan; Jia, Ziyuan; Ji, Liyu; Hang, Zhi Hong

    2017-12-01

    By exploiting the scaling invariance of photonic band diagrams, a complementary photonic crystal slab structure is realized by stacking two uniformly scaled double-zero-index dielectric photonic crystal slabs together. The space cancellation effect in complementary photonic crystals is demonstrated in both numerical simulations and microwave experiments. The refractive index dispersion of double-zero-index dielectric photonic crystal is experimentally measured. Using pure dielectrics, our photonic crystal structure will be an ideal platform to explore various intriguing properties related to a complementary medium.

  12. Complementary bowtie aperture for localizing and enhancing optical magnetic field

    Science.gov (United States)

    Zhou, Nan; Kinzel, Edward C.; Xu, Xianfan

    2011-08-01

    Nanoscale bowtie antenna and bowtie aperture antenna have been shown to generate strongly enhanced and localized electric fields below the diffraction limit in the optical frequency range. According to Babinet's principle, their complements will be efficient for concentrating and enhancing magnetic fields. In this Letter, we discuss the enhancement of magnetic field intensity of nanoscale complementary bowtie aperture as well as complementary bowtie aperture antenna, or diabolo nanoantenna. We show that the complementary bowtie antenna resonates at a smaller wavelength and thus is more suitable for applications near visible wavelengths. The near-field magnetic intensity can be further enhanced by the addition of groove structures that scatter surface plasmon.

  13. The Characterization of the Phlebotomus papatasi Transcriptome

    Science.gov (United States)

    2013-04-01

    Le. infantum (Li: CAM68214.1), Le. major (Lm: XP_001683430.1), Homo sapiens (Hs: AAD17527.1) and Bo. mori (Bm: NP_001108470.1). The WAG substitution...blood meals in Ph. langeroni (Dillon, El Kordy 1997). Here we have identified 23 unique Ph. papatasi sequences with high identity (BLASTP, əe-50) to...Perkin SAH, Caler E, Bonaldo MF, Soares MB, El -Sayeed N, Aksoy S. Analysis of fat body transcriptome from the adult tsetse fly, Glossina morsitans

  14. High density lipoprotein structural changes and drug response in lipidomic profiles following the long-term fenofibrate therapy in the FIELD substudy.

    Directory of Open Access Journals (Sweden)

    Laxman Yetukuri

    Full Text Available In a recent FIELD study the fenofibrate therapy surprisingly failed to achieve significant benefit over placebo in the primary endpoint of coronary heart disease events. Increased levels of atherogenic homocysteine were observed in some patients assigned to fenofibrate therapy but the molecular mechanisms behind this are poorly understood. Herein we investigated HDL lipidomic profiles associated with fenofibrate treatment and the drug-induced Hcy levels in the FIELD substudy. We found that fenofibrate leads to complex HDL compositional changes including increased apoA-II, diminishment of lysophosphatidylcholines and increase of sphingomyelins. Ethanolamine plasmalogens were diminished only in a subgroup of fenofibrate-treated patients with elevated homocysteine levels. Finally we performed molecular dynamics simulations to qualitatively reconstitute HDL particles in silico. We found that increased number of apoA-II excludes neutral lipids from HDL surface and apoA-II is more deeply buried in the lipid matrix than apoA-I. In conclusion, a detailed molecular characterization of HDL may provide surrogates for predictors of drug response and thus help identify the patients who might benefit from fenofibrate treatment.

  15. Lipidomics of Candida albicans biofilms reveals phase-dependent production of phospholipid molecular classes and role for lipid rafts in biofilm formation.

    Science.gov (United States)

    Lattif, Ali Abdul; Mukherjee, Pranab K; Chandra, Jyotsna; Roth, Mary R; Welti, Ruth; Rouabhia, Mahmoud; Ghannoum, Mahmoud A

    2011-11-01

    Candida albicans-associated bloodstream infections are linked to the ability of this yeast to form biofilms. In this study, we used lipidomics to compare the lipid profiles of C. albicans biofilms and planktonic cells, in early and mature developmental phases. Our results showed that significant differences exist in lipid composition in both developmental phases. Biofilms contained higher levels of phospholipid and sphingolipids than planktonic cells (nmol per g biomass, Pbiofilms compared to planktonic cells (P≤0.05). The ratio of phosphatidylcholine to phosphatidylethanolamine was lower in biofilms compared to planktonic cells in both early (1.17 vs 2.52, P≤0.001) and late (2.34 vs 3.81, P≤0.001) developmental phases. The unsaturation index of phospholipids decreased with time, with this effect being particularly strong for biofilms. Inhibition of the biosynthetic pathway for sphingolipid [mannosyl diinositolphosphoryl ceramide, M(IP)₂C] by myriocin or aureobasidin A, and disruption of the gene encoding inositolphosphotransferase (Ipt1p), abrogated the ability of C. albicans to form biofilms. The differences in lipid profiles between biofilms and planktonic Candida cells may have important implications for the biology and antifungal resistance of biofilms.

  16. Analysis of the liver lipidome reveals insights into the protective effect of exercise on high fat diet induced hepatosteatosis in mice

    DEFF Research Database (Denmark)

    Jordy, Andreas Børsting; Kraakman, Michael J; Gardner, Tim

    2015-01-01

    The accumulation of lipid at ectopic sites including the skeletal muscle and liver is a common consequence of obesity and is associated with tissue-specific and whole-body insulin resistance. Exercise is well known to improve insulin resistance by mechanisms not completely understood. We performe...... in fatty acid entry into hepatocytes. Given the important role of the liver in the regulation of whole body glucose homeostasis, hepatic lipid regression may be a key component by which exercise can improve metabolism.......The accumulation of lipid at ectopic sites including the skeletal muscle and liver is a common consequence of obesity and is associated with tissue-specific and whole-body insulin resistance. Exercise is well known to improve insulin resistance by mechanisms not completely understood. We performed...... lipidomic profiling via mass spectrometry in liver and skeletal muscle samples from exercise trained mice, to decipher the lipid changes associated with exercise-induced improvements in whole body glucose metabolism. Obesity and insulin resistance was induced in C57BL/6J mice by high fat feeding for four...

  17. Sleep Disorders and Complementary Health Approaches : What the Science Says

    Science.gov (United States)

    ... Sleep Disorders and Complementary Health Approaches: What the Science Says Share: April 2014 Clinical Guidelines, Scientific Literature, ... five randomized controlled trials evaluating the efficacy of music-assisted relaxation for sleep quality in adults found ...

  18. The initiation of complementary feeding among Qom indigenous people.

    Science.gov (United States)

    Olmedo, Sofia Irene; Valeggia, Claudia

    2014-06-01

    As of six months of life, breastfeeding no longer covers an infant's energy or micronutrient needs, so appropriate complementary feeding should be provided. The objective of this study was to assess the time and adequacy for introducing complementary feeding in a Qom/Toba population and analyze the sociocultural concepts of families regarding complementary feeding. Quantitative and qualitative data were collected by participant observation and semistructured surveys administered to mothers of 0-2 year old infants. Qom breastfeed their infants long term and on demand. Most infants have an adequate nutritional status and start complementary feeding at around 6 months old as per the local health center and international standards. However, mostly due to socioeconomic factors, foods chosen to complement breastfeeding have a relatively scarce nutritional value.

  19. The use of complementary and alternative therapies in childhood ...

    African Journals Online (AJOL)

    African Journal of Traditional, Complementary and Alternative Medicines ... based on a descriptive survey from the western black sea region of Turkey ... Materials and Methods: The study, of cross-sectional design, was conducted with the ...

  20. A complementary model for medical subspecialty training in South ...

    African Journals Online (AJOL)

    research was to develop a business model to complement the current academic ... larger-scale potential public-private partnerships (PPPs). The model ... complementary system, which will benefit both the private and the public sectors.

  1. Complementary and alternative medicine use in children with cystic fibrosis.

    Science.gov (United States)

    Giangioppo, Sandra; Kalaci, Odion; Radhakrishnan, Arun; Fleischer, Erin; Itterman, Jennifer; Lyttle, Brian; Price, April; Radhakrishnan, Dhenuka

    2016-11-01

    To estimate the overall prevalence of complementary and alternative medicine use among children with cystic fibrosis, determine specific modalities used, predictors of use and subjective helpfulness or harm from individual modalities. Of 53 children attending the cystic fibrosis clinic in London, Ontario (100% recruitment), 79% had used complementary and alternative medicine. The most commonly used modalities were air purifiers, humidifiers, probiotics, and omega-3 fatty acids. Family complementary and alternative medicine use was the only independent predictor of overall use. The majority of patients perceived benefit from specific modalities for cystic fibrosis symptoms. Given the high frequency and number of modalities used and lack of patient and disease characteristics predicting use, we recommend that health care providers should routinely ask about complementary and alternative medicine among all pediatric cystic fibrosis patients and assist patients in understanding the potential benefits and risks to make informed decisions about its use. Copyright © 2016 Elsevier Ltd. All rights reserved.

  2. Have complementary therapies demonstrated effectiveness in rheumatoid arthritis?

    Science.gov (United States)

    Fernández-Llanio Comella, Nagore; Fernández Matilla, Meritxell; Castellano Cuesta, Juan Antonio

    2016-01-01

    In recent decades the treatment of rheumatoid arthritis (RA) has improved thanks to the use of highly effective drugs. However, patients usually require long term therapy, which is not free of side effects. Therefore RA patients often demand complementary medicine, they seek additional sources of relief and/or less side effects. In fact 30-60% of rheumatic patients use some form of complementary medicine. Therefore, from conventional medicine, if we want to optimally treat our patients facilitating communication with them we must know the most commonly used complementary medicines. The aim of this review is to assess, based on published scientific research, what complementary therapies commonly used by patients with RA are effective and safe. Copyright © 2015 Elsevier España, S.L.U. and Sociedad Española de Reumatología y Colegio Mexicano de Reumatología. All rights reserved.

  3. Use of complementary and alternative medicine by patients with arthritis.

    Science.gov (United States)

    Unsal, Ayla; Gözüm, Sebahat

    2010-04-01

    The aims of this study were to determine the prevalence of complementary and alternative medicine use in patients with arthritis, the types of complementary and alternative medicine used, pertinent socio-demographic factors associated with complementary and alternative medicine use and its perceived efficacy. Arthritis is a major health issue, and the use of complementary and alternative medicine among patients with arthritis is common. This is a descriptive cross-sectional study. Data were obtained from 250 patients with arthritis at the physiotherapy and immunology clinics Atatürk University Hospital in eastern Turkey between May-July 2005 using a questionnaire developed specifically for this study. The instrument included questions on socio-demographic information, disease specifics and complementary and alternative medicine usage. Seventy-six per cent of participants reported use of at least one form of complementary and alternative medicine in the previous year. Complementary and alternative medicine users and non-users were not significantly different in most socio-demographic characteristics including age, gender, marital status and education level with the exception of economic status. We categorised treatment into six complementary and alternative medicine categories: 62.6% of patients used thermal therapies; 41.5% used oral herbal therapies; 40.5% used hot therapies; 32.6% used externally applied (skin) therapies; 28.4% used massage and 12.6% used cold therapies. All forms of complementary and alternative medicine except thermal and oral herbal therapies were perceived as very effective by more than half of study participants. Complementary and alternative medicine therapy is widely used by patients with arthritis and has perceived beneficial effects. It is important for nurses and other health care professionals to be knowledgeable about the use of complementary and alternative medicine therapies when providing care to patients with arthritis because of

  4. The Human Blood Metabolome-Transcriptome Interface

    Science.gov (United States)

    Schramm, Katharina; Adamski, Jerzy; Gieger, Christian; Herder, Christian; Carstensen, Maren; Peters, Annette; Rathmann, Wolfgang; Roden, Michael; Strauch, Konstantin; Suhre, Karsten; Kastenmüller, Gabi; Prokisch, Holger; Theis, Fabian J.

    2015-01-01

    Biological systems consist of multiple organizational levels all densely interacting with each other to ensure function and flexibility of the system. Simultaneous analysis of cross-sectional multi-omics data from large population studies is a powerful tool to comprehensively characterize the underlying molecular mechanisms on a physiological scale. In this study, we systematically analyzed the relationship between fasting serum metabolomics and whole blood transcriptomics data from 712 individuals of the German KORA F4 cohort. Correlation-based analysis identified 1,109 significant associations between 522 transcripts and 114 metabolites summarized in an integrated network, the ‘human blood metabolome-transcriptome interface’ (BMTI). Bidirectional causality analysis using Mendelian randomization did not yield any statistically significant causal associations between transcripts and metabolites. A knowledge-based interpretation and integration with a genome-scale human metabolic reconstruction revealed systematic signatures of signaling, transport and metabolic processes, i.e. metabolic reactions mainly belonging to lipid, energy and amino acid metabolism. Moreover, the construction of a network based on functional categories illustrated the cross-talk between the biological layers at a pathway level. Using a transcription factor binding site enrichment analysis, this pathway cross-talk was further confirmed at a regulatory level. Finally, we demonstrated how the constructed networks can be used to gain novel insights into molecular mechanisms associated to intermediate clinical traits. Overall, our results demonstrate the utility of a multi-omics integrative approach to understand the molecular mechanisms underlying both normal physiology and disease. PMID:26086077

  5. The Human Blood Metabolome-Transcriptome Interface.

    Directory of Open Access Journals (Sweden)

    Jörg Bartel

    2015-06-01

    Full Text Available Biological systems consist of multiple organizational levels all densely interacting with each other to ensure function and flexibility of the system. Simultaneous analysis of cross-sectional multi-omics data from large population studies is a powerful tool to comprehensively characterize the underlying molecular mechanisms on a physiological scale. In this study, we systematically analyzed the relationship between fasting serum metabolomics and whole blood transcriptomics data from 712 individuals of the German KORA F4 cohort. Correlation-based analysis identified 1,109 significant associations between 522 transcripts and 114 metabolites summarized in an integrated network, the 'human blood metabolome-transcriptome interface' (BMTI. Bidirectional causality analysis using Mendelian randomization did not yield any statistically significant causal associations between transcripts and metabolites. A knowledge-based interpretation and integration with a genome-scale human metabolic reconstruction revealed systematic signatures of signaling, transport and metabolic processes, i.e. metabolic reactions mainly belonging to lipid, energy and amino acid metabolism. Moreover, the construction of a network based on functional categories illustrated the cross-talk between the biological layers at a pathway level. Using a transcription factor binding site enrichment analysis, this pathway cross-talk was further confirmed at a regulatory level. Finally, we demonstrated how the constructed networks can be used to gain novel insights into molecular mechanisms associated to intermediate clinical traits. Overall, our results demonstrate the utility of a multi-omics integrative approach to understand the molecular mechanisms underlying both normal physiology and disease.

  6. Comparative Transcriptomics Among Four White Pine Species

    Directory of Open Access Journals (Sweden)

    Ethan A. G. Baker

    2018-05-01

    Full Text Available Conifers are the dominant plant species throughout the high latitude boreal forests as well as some lower latitude temperate forests of North America, Europe, and Asia. As such, they play an integral economic and ecological role across much of the world. This study focused on the characterization of needle transcriptomes from four ecologically important and understudied North American white pines within the Pinus subgenus Strobus. The populations of many Strobus species are challenged by native and introduced pathogens, native insects, and abiotic factors. RNA from the needles of western white pine (Pinus monticola, limber pine (Pinus flexilis, whitebark pine (Pinus albicaulis, and sugar pine (Pinus lambertiana was sampled, Illumina short read sequenced, and de novo assembled. The assembled transcripts and their subsequent structural and functional annotations were processed through custom pipelines to contend with the challenges of non-model organism transcriptome validation. Orthologous gene family analysis of over 58,000 translated transcripts, implemented through Tribe-MCL, estimated the shared and unique gene space among the four species. This revealed 2025 conserved gene families, of which 408 were aligned to estimate levels of divergence and reveal patterns of selection. Specific candidate genes previously associated with drought tolerance and white pine blister rust resistance in conifers were investigated.

  7. Analysis of a human brain transcriptome map

    Directory of Open Access Journals (Sweden)

    Greene Jonathan R

    2002-04-01

    Full Text Available Abstract Background Genome wide transcriptome maps can provide tools to identify candidate genes that are over-expressed or silenced in certain disease tissue and increase our understanding of the structure and organization of the genome. Expressed Sequence Tags (ESTs from the public dbEST and proprietary Incyte LifeSeq databases were used to derive a transcript map in conjunction with the working draft assembly of the human genome sequence. Results Examination of ESTs derived from brain tissues (excluding brain tumor tissues suggests that these genes are distributed on chromosomes in a non-random fashion. Some regions on the genome are dense with brain-enriched genes while some regions lack brain-enriched genes, suggesting a significant correlation between distribution of genes along the chromosome and tissue type. ESTs from brain tumor tissues have also been mapped to the human genome working draft. We reveal that some regions enriched in brain genes show a significant decrease in gene expression in brain tumors, and, conversely that some regions lacking in brain genes show an increased level of gene expression in brain tumors. Conclusions This report demonstrates a novel approach for tissue specific transcriptome mapping using EST-based quantitative assessment.

  8. Crx broadly modulates the pineal transcriptome

    DEFF Research Database (Denmark)

    Rovsing, Louise; Clokie, Samuel; Bustos, Diego M

    2011-01-01

    Cone-rod homeobox (Crx) encodes Crx, a transcription factor expressed selectively in retinal photoreceptors and pinealocytes, the major cell type of the pineal gland. In this study, the influence of Crx on the mammalian pineal gland was studied by light and electron microscopy and by use of micro......Cone-rod homeobox (Crx) encodes Crx, a transcription factor expressed selectively in retinal photoreceptors and pinealocytes, the major cell type of the pineal gland. In this study, the influence of Crx on the mammalian pineal gland was studied by light and electron microscopy and by use......-type animals; only eight of these were also day/night expressed in the Crx-/- pineal gland. However, in the Crx-/- pineal gland 41 genes exhibited differential night/day expression that was not seen in wild-type animals. These findings indicate that Crx broadly modulates the pineal transcriptome and also...... influences differential night/day gene expression in this tissue. Some effects of Crx deletion on the pineal transcriptome might be mediated by Hoxc4 up-regulation....

  9. 76 FR 6487 - National Center for Complementary and Alternative Medicine; Announcement of Workshop on...

    Science.gov (United States)

    2011-02-04

    ... Complementary and Alternative Medicine; Announcement of Workshop on Clarifying Directions and Approaches to...: The National Center for Complementary and Alternative Medicine (NCCAM) invites the research [email protected] . Background: The National Center for Complementary and Alternative Medicine (NCCAM) was...

  10. 75 FR 52357 - Request for Comment: National Center for Complementary and Alternative Medicine Draft Strategic Plan

    Science.gov (United States)

    2010-08-25

    ...: National Center for Complementary and Alternative Medicine Draft Strategic Plan ACTION: Notice. SUMMARY: The National Center for Complementary and Alternative Medicine (NCCAM) is developing its third... for Complementary and Alternative Medicine (NCCAM) was established in 1998 with the mission of...

  11. 77 FR 31862 - National Center for Complementary & Alternative Medicine; Notice of Closed Meetings

    Science.gov (United States)

    2012-05-30

    ... Complementary & Alternative Medicine; Notice of Closed Meetings Pursuant to section 10(d) of the Federal... Scientific Review, National Center for Complementary and Alternative Medicine, NIH, 6707 Democracy Blvd... for Complementary and Alternative Medicine Special Emphasis Panel; HCS Collaboratory Pragmatic Trials...

  12. Complementary Set Matrices Satisfying a Column Correlation Constraint

    OpenAIRE

    Wu, Di; Spasojevic, Predrag

    2006-01-01

    Motivated by the problem of reducing the peak to average power ratio (PAPR) of transmitted signals, we consider a design of complementary set matrices whose column sequences satisfy a correlation constraint. The design algorithm recursively builds a collection of $2^{t+1}$ mutually orthogonal (MO) complementary set matrices starting from a companion pair of sequences. We relate correlation properties of column sequences to that of the companion pair and illustrate how to select an appropriate...

  13. Complementary Medicine Journal of Faculty of Nursing and Midwifery

    OpenAIRE

    Seraji; Vakilian

    2011-01-01

    Introduction: Half of the pregnant women suffer from the excruciating degrees of labor pain. Nowadays, however, the use of painkillers for decreasing labor pain due to their adverse effects on the mother and child is less common and attention has been shifted towards non-medical methods and complementary medicine such as message therapy, acupuncture, hydrotherapy, and herbal medicine. One of the branches of complementary medicine is hydrotherapy with herbal essences. Breathing techniques, on ...

  14. Complementary and alternative medicine use in children with thalassaemia.

    Science.gov (United States)

    Efe, Emine; Işler, Ayşegül; Sarvan, Süreyya; Başer, Hayriye; Yeşilipek, Akif

    2013-03-01

    The aims of this study were to: (1) determine the types of complementary and alternative medicine use among children with thalassaemia as reported by parents and (2) describe sociodemographic and medical factors associated with the use of such treatments in families residing in southern Turkey. Thalassaemia is one of the most common human genetic diseases. Despite the therapeutic efforts, patients will encounter a variety of physical and psychological problems. Therefore, the use of complementary and alternative medicines among children thalassaemia is becoming increasingly popular. This is a descriptive study of complementary and alternative medicine. This study was conducted in the Hematology Outpatient Clinic at Akdeniz University Hospital and in the Thalassemia Centre at Ministry of Health Antalya Education and Research Hospital, Antalya, Turkey, between January 2010-December 2010. Parents of 97 paediatric patients, among 125 parents who applied to the haematology outpatient clinic and thalassaemia centre between these dates, agreed to take part in the study with whom contact could be made were included. Data were collected by using a questionnaire. The proportion of parents who reported using one or more of the complementary and alternative medicine methods was 82·5%. Of these parents, 61·8% were using prayer/spiritual practice, 47·4% were using nutritional supplements and 35·1% were using animal materials. It was determined that a significant portion of the parents using complementary and alternative medicine use it to treat their children's health problems, they were informed about complementary and alternative medicine by their paediatricians and family elders, and they have discussed the use of complementary and alternative medicine with healthcare professionals. To sustain medical treatment and prognosis of thalassaemia, it is important for nurses to consult with their patients and parents regarding the use and potential risks of some complementary

  15. Supramolecular Assembly of Complementary Cyanine Salt J-Aggregates

    KAUST Repository

    Li, Zhong’ an; Mukhopadhyay, Sukrit; Jang, Sei-Hum; Bredas, Jean-Luc; Jen, Alex K.-Y.

    2015-01-01

    An understanding of structure–property relationships in cyanine dyes is critical for their design and application. Anionic and cationic cyanines can be organized into complementary cyanine salts, offering potential building blocks to modulate their intra/intermolecular interactions in the solid state. Here, we demonstrate how the structures of these complementary salts can be tuned to achieve highly ordered J-type supramolecular aggregate structures of heptamethine dyes in crystalline solids.

  16. The Liquidity Coverage Ratio: the need for further complementary ratios?

    OpenAIRE

    Ojo, Marianne

    2013-01-01

    This paper considers components of the Liquidity Coverage Ratio – as well as certain prevailing gaps which may necessitate the introduction of a complementary liquidity ratio. The definitions and objectives accorded to the Liquidity Coverage Ratio (LCR) and Net Stable Funding Ratio (NSFR) highlight the focus which is accorded to time horizons for funding bank operations. A ratio which would focus on the rate of liquidity transformations and which could also serve as a complementary metric gi...

  17. Supramolecular Assembly of Complementary Cyanine Salt J-Aggregates

    KAUST Repository

    Li, Zhong’an

    2015-09-09

    An understanding of structure–property relationships in cyanine dyes is critical for their design and application. Anionic and cationic cyanines can be organized into complementary cyanine salts, offering potential building blocks to modulate their intra/intermolecular interactions in the solid state. Here, we demonstrate how the structures of these complementary salts can be tuned to achieve highly ordered J-type supramolecular aggregate structures of heptamethine dyes in crystalline solids.

  18. Chinese Cyber Espionage: A Complementary Method to Aid PLA Modernization

    Science.gov (United States)

    2015-12-01

    COMPLEMENTARY METHOD TO AID PLA MODERNIZATION by Jamie M. Ellis December 2015 Thesis Advisor: Wade L. Huntley Second Reader: Christopher R. Twomey THIS...Master’s Thesis 4. TITLE AND SUBTITLE CHINESE CYBER ESPIONAGE: A COMPLEMENTARY METHOD TO AID PLA MODERNIZATION 5. FUNDING NUMBERS 6. AUTHOR(S) Jamie M...DISTRIBUTION CODE A 13. ABSTRACT (maximum 200 words) In 2013, Mandiant published a report linking one People’s Liberation Army ( PLA ) unit to the

  19. TRAM (Transcriptome Mapper: database-driven creation and analysis of transcriptome maps from multiple sources

    Directory of Open Access Journals (Sweden)

    Danieli Gian

    2011-02-01

    Full Text Available Abstract Background Several tools have been developed to perform global gene expression profile data analysis, to search for specific chromosomal regions whose features meet defined criteria as well as to study neighbouring gene expression. However, most of these tools are tailored for a specific use in a particular context (e.g. they are species-specific, or limited to a particular data format and they typically accept only gene lists as input. Results TRAM (Transcriptome Mapper is a new general tool that allows the simple generation and analysis of quantitative transcriptome maps, starting from any source listing gene expression values for a given gene set (e.g. expression microarrays, implemented as a relational database. It includes a parser able to assign univocal and updated gene symbols to gene identifiers from different data sources. Moreover, TRAM is able to perform intra-sample and inter-sample data normalization, including an original variant of quantile normalization (scaled quantile, useful to normalize data from platforms with highly different numbers of investigated genes. When in 'Map' mode, the software generates a quantitative representation of the transcriptome of a sample (or of a pool of samples and identifies if segments of defined lengths are over/under-expressed compared to the desired threshold. When in 'Cluster' mode, the software searches for a set of over/under-expressed consecutive genes. Statistical significance for all results is calculated with respect to genes localized on the same chromosome or to all genome genes. Transcriptome maps, showing differential expression between two sample groups, relative to two different biological conditions, may be easily generated. We present the results of a biological model test, based on a meta-analysis comparison between a sample pool of human CD34+ hematopoietic progenitor cells and a sample pool of megakaryocytic cells. Biologically relevant chromosomal segments and gene

  20. The developmental transcriptome of Drosophila melanogaster

    Energy Technology Data Exchange (ETDEWEB)

    University of Connecticut; Graveley, Brenton R.; Brooks, Angela N.; Carlson, Joseph W.; Duff, Michael O.; Landolin, Jane M.; Yang, Li; Artieri, Carlo G.; van Baren, Marijke J.; Boley, Nathan; Booth, Benjamin W.; Brown, James B.; Cherbas, Lucy; Davis, Carrie A.; Dobin, Alex; Li, Renhua; Lin, Wei; Malone, John H.; Mattiuzzo, Nicolas R.; Miller, David; Sturgill, David; Tuch, Brian B.; Zaleski, Chris; Zhang, Dayu; Blanchette, Marco; Dudoit, Sandrine; Eads, Brian; Green, Richard E.; Hammonds, Ann; Jiang, Lichun; Kapranov, Phil; Langton, Laura; Perrimon, Norbert; Sandler, Jeremy E.; Wan, Kenneth H.; Willingham, Aarron; Zhang, Yu; Zou, Yi; Andrews, Justen; Bicke, Peter J.; Brenner, Steven E.; Brent, Michael R.; Cherbas, Peter; Gingeras, Thomas R.; Hoskins, Roger A.; Kaufman, Thomas C.; Oliver, Brian; Celniker, Susan E.

    2010-12-02

    Drosophila melanogaster is one of the most well studied genetic model organisms; nonetheless, its genome still contains unannotated coding and non-coding genes, transcripts, exons and RNA editing sites. Full discovery and annotation are pre-requisites for understanding how the regulation of transcription, splicing and RNA editing directs the development of this complex organism. Here we used RNA-Seq, tiling microarrays and cDNA sequencing to explore the transcriptome in 30 distinct developmental stages. We identified 111,195 new elements, including thousands of genes, coding and non-coding transcripts, exons, splicing and editing events, and inferred protein isoforms that previously eluded discovery using established experimental, prediction and conservation-based approaches. These data substantially expand the number of known transcribed elements in the Drosophila genome and provide a high-resolution view of transcriptome dynamics throughout development. Drosophila melanogaster is an important non-mammalian model system that has had a critical role in basic biological discoveries, such as identifying chromosomes as the carriers of genetic information and uncovering the role of genes in development. Because it shares a substantial genic content with humans, Drosophila is increasingly used as a translational model for human development, homeostasis and disease. High-quality maps are needed for all functional genomic elements. Previous studies demonstrated that a rich collection of genes is deployed during the life cycle of the fly. Although expression profiling using microarrays has revealed the expression of, 13,000 annotated genes, it is difficult to map splice junctions and individual base modifications generated by RNA editing using such approaches. Single-base resolution is essential to define precisely the elements that comprise the Drosophila transcriptome. Estimates of the number of transcript isoforms are less accurate than estimates of the number of genes

  1. Complementary Hand Responses Occur in Both Peri- and Extrapersonal Space.

    Directory of Open Access Journals (Sweden)

    Tim W Faber

    Full Text Available Human beings have a strong tendency to imitate. Evidence from motor priming paradigms suggests that people automatically tend to imitate observed actions such as hand gestures by performing mirror-congruent movements (e.g., lifting one's right finger upon observing a left finger movement; from a mirror perspective. Many observed actions however, do not require mirror-congruent responses but afford complementary (fitting responses instead (e.g., handing over a cup; shaking hands. Crucially, whereas mirror-congruent responses don't require physical interaction with another person, complementary actions often do. Given that most experiments studying motor priming have used stimuli devoid of contextual information, this space or interaction-dependency of complementary responses has not yet been assessed. To address this issue, we let participants perform a task in which they had to mirror or complement a hand gesture (fist or open hand performed by an actor depicted either within or outside of reach. In three studies, we observed faster reaction times and less response errors for complementary relative to mirrored hand movements in response to open hand gestures (i.e., 'hand-shaking' irrespective of the perceived interpersonal distance of the actor. This complementary effect could not be accounted for by a low-level spatial cueing effect. These results demonstrate that humans have a strong and automatic tendency to respond by performing complementary actions. In addition, our findings underline the limitations of manipulations of space in modulating effects of motor priming and the perception of affordances.

  2. Complementary Hand Responses Occur in Both Peri- and Extrapersonal Space.

    Science.gov (United States)

    Faber, Tim W; van Elk, Michiel; Jonas, Kai J

    2016-01-01

    Human beings have a strong tendency to imitate. Evidence from motor priming paradigms suggests that people automatically tend to imitate observed actions such as hand gestures by performing mirror-congruent movements (e.g., lifting one's right finger upon observing a left finger movement; from a mirror perspective). Many observed actions however, do not require mirror-congruent responses but afford complementary (fitting) responses instead (e.g., handing over a cup; shaking hands). Crucially, whereas mirror-congruent responses don't require physical interaction with another person, complementary actions often do. Given that most experiments studying motor priming have used stimuli devoid of contextual information, this space or interaction-dependency of complementary responses has not yet been assessed. To address this issue, we let participants perform a task in which they had to mirror or complement a hand gesture (fist or open hand) performed by an actor depicted either within or outside of reach. In three studies, we observed faster reaction times and less response errors for complementary relative to mirrored hand movements in response to open hand gestures (i.e., 'hand-shaking') irrespective of the perceived interpersonal distance of the actor. This complementary effect could not be accounted for by a low-level spatial cueing effect. These results demonstrate that humans have a strong and automatic tendency to respond by performing complementary actions. In addition, our findings underline the limitations of manipulations of space in modulating effects of motor priming and the perception of affordances.

  3. Sequencing and analysis of the Mediterranean amphioxus (Branchiostoma lanceolatum transcriptome.

    Directory of Open Access Journals (Sweden)

    Silvan Oulion

    Full Text Available BACKGROUND: The basally divergent phylogenetic position of amphioxus (Cephalochordata, as well as its conserved morphology, development and genetics, make it the best proxy for the chordate ancestor. Particularly, studies using the amphioxus model help our understanding of vertebrate evolution and development. Thus, interest for the amphioxus model led to the characterization of both the transcriptome and complete genome sequence of the American species, Branchiostoma floridae. However, recent technical improvements allowing induction of spawning in the laboratory during the breeding season on a daily basis with the Mediterranean species Branchiostoma lanceolatum have encouraged European Evo-Devo researchers to adopt this species as a model even though no genomic or transcriptomic data have been available. To fill this need we used the pyrosequencing method to characterize the B. lanceolatum transcriptome and then compared our results with the published transcriptome of B. floridae. RESULTS: Starting with total RNA from nine different developmental stages of B. lanceolatum, a normalized cDNA library was constructed and sequenced on Roche GS FLX (Titanium mode. Around 1.4 million of reads were produced and assembled into 70,530 contigs (average length of 490 bp. Overall 37% of the assembled sequences were annotated by BlastX and their Gene Ontology terms were determined. These results were then compared to genomic and transcriptomic data of B. floridae to assess similarities and specificities of each species. CONCLUSION: We obtained a high-quality amphioxus (B. lanceolatum reference transcriptome using a high throughput sequencing approach. We found that 83% of the predicted genes in the B. floridae complete genome sequence are also found in the B. lanceolatum transcriptome, while only 41% were found in the B. floridae transcriptome obtained with traditional Sanger based sequencing. Therefore, given the high degree of sequence conservation

  4. [Alternative and complementary medicine from the primary care physician's viewpoint].

    Science.gov (United States)

    Soós, Sándor Árpád; Eőry, Ajándék; Eőry, Ajándok; Harsányi, László; Kalabay, László

    2015-07-12

    The patients initiate the use of complementary and alternative medicine and this often remains hidden from their primary care physician. To explore general practitioners' knowledge and attitude towards complementary and alternative medicine, and study the need and appropriate forms of education, as well as ask their opinion on integration of alternative medicine into mainstream medicine. A voluntary anonymous questionnaire was used on two conferences for general practitioners organized by the Family Medicine Department of Semmelweis University. Complementary and alternative medicine was defined by the definition of the Hungarian Academy of Sciences and certified modalities were all listed. 194 general practitioners answered the questionnaire (39.8% response rate). 14% of the responders had licence in at least one of the complementary and alternative therapies, 45% used complementary and alternative therapy in their family in case of illness. It was the opinion of the majority (91.8%) that it was necessary to be familiar with every method used by their patients, however, 82.5% claimed not to have enough knowledge in complementary medicine. Graduate and postgraduate education in the field was thought to be necessary by 86% of the responders; increased odds for commitment in personal education was found among female general practitioners, less than 20 years professional experience and personal experience of alternative medicine. These data suggest that general practitioners would like to know more about complementary and alternative medicine modalities used by their patients. They consider education of medical professionals necessary and a special group is willing to undergo further education in the field.

  5. Peroxidase gene discovery from the horseradish transcriptome.

    Science.gov (United States)

    Näätsaari, Laura; Krainer, Florian W; Schubert, Michael; Glieder, Anton; Thallinger, Gerhard G

    2014-03-24

    Horseradish peroxidases (HRPs) from Armoracia rusticana have long been utilized as reporters in various diagnostic assays and histochemical stainings. Regardless of their increasing importance in the field of life sciences and suggested uses in medical applications, chemical synthesis and other industrial applications, the HRP isoenzymes, their substrate specificities and enzymatic properties are poorly characterized. Due to lacking sequence information of natural isoenzymes and the low levels of HRP expression in heterologous hosts, commercially available HRP is still extracted as a mixture of isoenzymes from the roots of A. rusticana. In this study, a normalized, size-selected A. rusticana transcriptome library was sequenced using 454 Titanium technology. The resulting reads were assembled into 14871 isotigs with an average length of 1133 bp. Sequence databases, ORF finding and ORF characterization were utilized to identify peroxidase genes from the 14871 isotigs generated by de novo assembly. The sequences were manually reviewed and verified with Sanger sequencing of PCR amplified genomic fragments, resulting in the discovery of 28 secretory peroxidases, 23 of them previously unknown. A total of 22 isoenzymes including allelic variants were successfully expressed in Pichia pastoris and showed peroxidase activity with at least one of the substrates tested, thus enabling their development into commercial pure isoenzymes. This study demonstrates that transcriptome sequencing combined with sequence motif search is a powerful concept for the discovery and quick supply of new enzymes and isoenzymes from any plant or other eukaryotic organisms. Identification and manual verification of the sequences of 28 HRP isoenzymes do not only contribute a set of peroxidases for industrial, biological and biomedical applications, but also provide valuable information on the reliability of the approach in identifying and characterizing a large group of isoenzymes.

  6. The human airway epithelial basal cell transcriptome.

    Directory of Open Access Journals (Sweden)

    Neil R Hackett

    2011-05-01

    Full Text Available The human airway epithelium consists of 4 major cell types: ciliated, secretory, columnar and basal cells. During natural turnover and in response to injury, the airway basal cells function as stem/progenitor cells for the other airway cell types. The objective of this study is to better understand human airway epithelial basal cell biology by defining the gene expression signature of this cell population.Bronchial brushing was used to obtain airway epithelium from healthy nonsmokers. Microarrays were used to assess the transcriptome of basal cells purified from the airway epithelium in comparison to the transcriptome of the differentiated airway epithelium. This analysis identified the "human airway basal cell signature" as 1,161 unique genes with >5-fold higher expression level in basal cells compared to differentiated epithelium. The basal cell signature was suppressed when the basal cells differentiated into a ciliated airway epithelium in vitro. The basal cell signature displayed overlap with genes expressed in basal-like cells from other human tissues and with that of murine airway basal cells. Consistent with self-modulation as well as signaling to other airway cell types, the human airway basal cell signature was characterized by genes encoding extracellular matrix components, growth factors and growth factor receptors, including genes related to the EGF and VEGF pathways. Interestingly, while the basal cell signature overlaps that of basal-like cells of other organs, the human airway basal cell signature has features not previously associated with this cell type, including a unique pattern of genes encoding extracellular matrix components, G protein-coupled receptors, neuroactive ligands and receptors, and ion channels.The human airway epithelial basal cell signature identified in the present study provides novel insights into the molecular phenotype and biology of the stem/progenitor cells of the human airway epithelium.

  7. A transcriptome anatomy of human colorectal cancers

    International Nuclear Information System (INIS)

    Lü, Bingjian; Xu, Jing; Lai, Maode; Zhang, Hao; Chen, Jian

    2006-01-01

    Accumulating databases in human genome research have enabled integrated genome-wide study on complicated diseases such as cancers. A practical approach is to mine a global transcriptome profile of disease from public database. New concepts of these diseases might emerge by landscaping this profile. In this study, we clustered human colorectal normal mucosa (N), inflammatory bowel disease (IBD), adenoma (A) and cancer (T) related expression sequence tags (EST) into UniGenes via an in-house GetUni software package and analyzed the transcriptome overview of these libraries by GOTree Machine (GOTM). Additionally, we downloaded UniGene based cDNA libraries of colon and analyzed them by Xprofiler to cross validate the efficiency of GetUni. Semi-quantitative RT-PCR was used to validate the expression of β-catenin and. 7 novel genes in colorectal cancers. The efficiency of GetUni was successfully validated by Xprofiler and RT-PCR. Genes in library N, IBD and A were all found in library T. A total of 14,879 genes were identified with 2,355 of them having at least 2 transcripts. Differences in gene enrichment among these libraries were statistically significant in 50 signal transduction pathways and Pfam protein domains by GOTM analysis P < 0.01 Hypergeometric Test). Genes in two metabolic pathways, ribosome and glycolysis, were more enriched in the expression profiles of A and IBD than in N and T. Seven transmembrane receptor superfamily genes were typically abundant in cancers. Colorectal cancers are genetically heterogeneous. Transcription variants are common in them. Aberrations of ribosome and glycolysis pathway might be early indicators of precursor lesions in colon cancers. The electronic gene expression profile could be used to highlight the integral molecular events in colorectal cancers

  8. Transcriptome sequences resolve deep relationships of the grape family.

    Science.gov (United States)

    Wen, Jun; Xiong, Zhiqiang; Nie, Ze-Long; Mao, Likai; Zhu, Yabing; Kan, Xian-Zhao; Ickert-Bond, Stefanie M; Gerrath, Jean; Zimmer, Elizabeth A; Fang, Xiao-Dong

    2013-01-01

    Previous phylogenetic studies of the grape family (Vitaceae) yielded poorly resolved deep relationships, thus impeding our understanding of the evolution of the family. Next-generation sequencing now offers access to protein coding sequences very easily, quickly and cost-effectively. To improve upon earlier work, we extracted 417 orthologous single-copy nuclear genes from the transcriptomes of 15 species of the Vitaceae, covering its phylogenetic diversity. The resulting transcriptome phylogeny provides robust support for the deep relationships, showing the phylogenetic utility of transcriptome data for plants over a time scale at least since the mid-Cretaceous. The pros and cons of transcriptome data for phylogenetic inference in plants are also evaluated.

  9. Transcriptome sequences resolve deep relationships of the grape family.

    Directory of Open Access Journals (Sweden)

    Jun Wen

    Full Text Available Previous phylogenetic studies of the grape family (Vitaceae yielded poorly resolved deep relationships, thus impeding our understanding of the evolution of the family. Next-generation sequencing now offers access to protein coding sequences very easily, quickly and cost-effectively. To improve upon earlier work, we extracted 417 orthologous single-copy nuclear genes from the transcriptomes of 15 species of the Vitaceae, covering its phylogenetic diversity. The resulting transcriptome phylogeny provides robust support for the deep relationships, showing the phylogenetic utility of transcriptome data for plants over a time scale at least since the mid-Cretaceous. The pros and cons of transcriptome data for phylogenetic inference in plants are also evaluated.

  10. Illumina–based de novo transcriptome sequencing and analysis of ...

    Indian Academy of Sciences (India)

    Administrator

    2017-10-25

    Oct 25, 2017 ... (Shanghai, China) following manufacturer's protocols (Illumina, San .... suggests that pathways involved in musk production are expressed at a ..... Strickler S. R., Aureliano B. and Mueller L. A. 2012 Designing a transcriptome.

  11. Design of organic complementary circuits and systems on foil

    CERN Document Server

    Abdinia, Sahel; Cantatore, Eugenio

    2015-01-01

    This book describes new approaches to fabricate complementary organic electronics, and focuses on the design of circuits and practical systems created using these manufacturing approaches. The authors describe two state-of-the-art, complementary organic technologies, characteristics and modeling of their transistors and their capability to implement circuits and systems on foil. Readers will benefit from the valuable overview of the challenges and opportunities that these extremely innovative technologies provide. ·         Demonstrates first circuits implemented using specific complementary organic technologies, including first printed analog to digital converter, first dynamic logic on foil and largest complementary organic circuit ·         Includes step-by-step design from single transistor level to complete systems on foil ·         Provides a platform for comparing state-of-the-art complementary organic technologies and for comparing these with other similar technologies, spec...

  12. Determination of complementary therapies for prevention of striae gravidarum

    Directory of Open Access Journals (Sweden)

    Gamze Teskereci

    2018-03-01

    Full Text Available Background and Design: Striae gravidarum (SG has been reported to be associated with various factors, but the role of complementary therapies in the prevention of SG is still not well understood. The aim of this study was to determine complementary therapies for prevention of SG. Materials and Methods: This descriptive research was conducted on 120 pregnant women in a maternity clinic at a university hospital. Of 120 women, 49 were going through the last trimester and 71 were going through their first postpartum 24 hours. Data were collected using a 25-item-questionnaire through face-to-face interviews between June and July in 2016. Obtained data were evaluated by using descriptive statistics, chi-square test and the Kruskal-Wallis test. Results: 90.8% of women had SG. For the prevention of SG, 46.7% of women used massage, a manipulative body-based complementary therapy, 55.2% used oils, 28.6% used creams and 8.0% used a mixture of creams and oils for massaging. 42.9% of women started to use complementary therapies in their first trimester. Half of the women stated that they had received information about complementary therapies. A significantly lower rate of women using massage had SG compared to those not using massage (p=0.023. Conclusion: It was concluded that nearly half of the women used massage for the prevention of SG. In addition, massage application was found to reduce the occurrence of SG.

  13. Complementary therapy use by women's health clinic clients.

    Science.gov (United States)

    Pettigrew, Amy C; King, Margaret O'Brien; McGee, Karen; Rudolph, Connie

    2004-01-01

    While it is known that more women than men use complementary and alternative therapies, it is important to look at women who are pregnant or possibly receiving hormonal therapy, as side effects and consequences of these therapies may have a significant effect on their health status. To assess women's knowledge, perceived effectiveness and use of 20 complementary and alternative therapies. Descriptive four-page questionnaire to obtain data on the use, reason for use, knowledge, perceived effectiveness, and sources of information of twenty complementary and alternative therapies. Women's Health Center at a large Midwestern hospital. A convenience sample of 250 women waiting to be seen by either a nurse midwife or obstetrician/gynecologist at an outpatient clinic. Sixty-nine percent of the participants used one or more complementary therapy. The most frequently used therapies included prayer, vitamins, massage, diet, and aromatherapy. The best predictor of use of each therapy was the participant's knowledge of the therapy. Participants generally rated the efficacy of the therapies higher than their knowledge level. Frequently cited sources of information were popular media and family. The least common information sources were nurse-midwives, drug stores, Internet, and other professional healthcare providers. Women in this setting use complementary therapies at a rate greater than the general population. The participants obtained a great deal of their information about the therapies from popular press, media, friends, and family members rather than from licensed healthcare providers.

  14. An emerging picture of the seed desiccome: confirmed regulators and newcomers identified using transcriptome comparison

    Directory of Open Access Journals (Sweden)

    Emmanuel eTerrasson

    2013-12-01

    Full Text Available Desiccation tolerance (DT is the capacity to withstand total loss of cellular water. It is acquired during seed filling and lost just after germination. However, in many species, a germinated seed can regain DT under adverse conditions such as osmotic stress. The genes, proteins and metabolites that are required to establish this DT is referred to as the desiccome. It includes both a range of protective mechanisms and underlying regulatory pathways that remain poorly understood. As a first step towards the identification of the seed desiccome of Medicago truncatula, using updated microarrays we characterised the overlapping transcriptomes associated with acquisition of DT in developing seeds and the re-establishment of DT in germinated seeds using a polyethylene glycol treatment (-1.7 MPa. The resulting list contained 740 and 2829 transcripts whose levels respectively increased and decreased with DT. Fourty-eight transcription factors were identified including MtABI3, MtABI5 and many genes regulating flowering transition and cell identity. A promoter enrichment analysis revealed a strong over-representation of ABRE elements together with light-responsive cis-acting elements. In Mtabi5 Tnt1 insertion mutants, DT could no longer be re-established by an osmotic stress. Transcriptome analysis on Mtabi5 radicles during osmotic stress revealed that 13 and 15 % of the up-regulated and down-regulated genes, respectively, are mis-regulated in the mutants and might be putative downstream targets of MtABI5 implicated in the re-establishment of DT. Likewise, transcriptome comparisons of the desiccation sensitive Mtabi3 mutants and hairy roots ectopically expressing MtABI3 revealed that 35% and 23% of the up-regulated and down-regulated genes are acting downstream of MtABI3. Our data suggest that ABI3 and ABI5 have complementary roles in DT. Whether DT evolved by co-opting existing pathways regulating flowering and cellular phase transition and cell identity

  15. Genome Annotation and Transcriptomics of Oil-Producing Algae

    Science.gov (United States)

    2015-03-16

    AFRL-OSR-VA-TR-2015-0103 GENOME ANNOTATION AND TRANSCRIPTOMICS OF OIL-PRODUCING ALGAE Sabeeha Merchant UNIVERSITY OF CALIFORNIA LOS ANGELES Final...2010 To 12-31-2014 4. TITLE AND SUBTITLE GENOME ANNOTATION AND TRANSCRIPTOMICS OF OIL-PRODUCING ALGAE 5a. CONTRACT NUMBER FA9550-10-1-0095 5b...NOTES 14. ABSTRACT Most algae accumulate triacylglycerols (TAGs) when they are starved for essential nutrients like N, S, P (or Si in the case of some

  16. ALTERATIONS IN THE DEVELOPING TESTIS TRANSCRIPTOME FOLLOWING EMBRYONIC VINCLOZOLIN EXPOSURE

    OpenAIRE

    Clement, Tracy M.; Savenkova, Marina I.; Settles, Matthew; Anway, Matthew D.; Skinner, Michael K.

    2010-01-01

    The current study investigates the direct effects of in utero vinclozolin exposure on the developing F1 generation rat testis transcriptome. Previous studies have demonstrated that exposure to vinclozolin during embryonic gonadal sex determination induces epigenetic modifications of the germ line and transgenerational adult onset disease states. Microarray analyses were performed to compare control and vinclozolin treated testis transcriptomes at embryonic day 13, 14 and 16. A total of 576 di...

  17. Assessment of the effects of As(III) treatment on cyanobacteria lipidomic profiles by LC-MS and MCR-ALS.

    Science.gov (United States)

    Marques, Aline S; Bedia, Carmen; Lima, Kássio M G; Tauler, Romà

    2016-08-01

    Cyanobacteria are a group of photosynthetic, nitrogen-fixing bacteria present in a wide variety of habitats such as freshwater, marine, and terrestrial ecosystems. In this work, the effects of As(III), a major toxic environmental pollutant, on the lipidomic profiles of two cyanobacteria species (Anabaena and Planktothrix agardhii) were assessed by means of a recently proposed method based on the concept of regions of interest (ROI) in liquid chromatography mass spectroscopy (LC-MS) together with multivariate curve resolution alternating least squares (MCR-ALS). Cyanobacteria were exposed to two concentrations of As(III) for a week, and lipid extracts were analyzed by ultrahigh-performance liquid chromatography/time-of-flight mass spectrometry in full scan mode. The data obtained were compressed by means of the ROI strategy, and the resulting LC-MS data sets were analyzed by the MCR-ALS method. Comparison of profile peak areas resolved by MCR-ALS in control and exposed samples allowed the discrimination of lipids whose concentrations were changed due to As(III) treatment. The tentative identification of these lipids revealed an important reduction of the levels of some galactolipids such as monogalactosyldiacylglycerol, the pigment chlorophyll a and its degradation product, pheophytin a, as well as carotene compounds such as 3-hydroxycarotene and carotene-3,3'-dione, all of these compounds being essential in the photosynthetic process. These results suggested that As(III) induced important changes in the composition of lipids of cyanobacteria, which were able to compromise their energy production processes. Graphical abstract Steps of the proposed LC-MS + MCR-ALS procedure.

  18. Matrix-assisted laser desorption/ionization mass spectrometry imaging of cell cultures for the lipidomic analysis of potential lipid markers in human breast cancer invasion.

    Science.gov (United States)

    Wang, Shujuan; Chen, Xiaowu; Luan, Hemi; Gao, Dan; Lin, Shuhai; Cai, Zongwei; Liu, Jianjun; Liu, Hongxia; Jiang, Yuyang

    2016-02-28

    Breast cancer is the leading cause of cancer death among women worldwide. Identification of lipid targets that play a role in breast cancer invasion may advance our understanding of the rapid progression of cancer and may lead to the development of new biomarkers for the disease. Matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI MSI) was applied for the lipidomic profiling of two poorly invasive and two highly invasive breast cancer cell lines to identify the differentially accumulated lipids related to the invasive phenotype. The four cell lines were individually grown on indium tin oxide (ITO)-coated glass slides, analyzed as cell cultures. The raster width and matrix for detection were optimized to improve detection sensitivity. Optimized MSI measurements were performed directly on the cell culture with 9-aminoacridine as matrix, resulting in 215 endogenous compounds detected in positive ion mode and 267 endogenous compounds in negative ion mode in all the four cell lines, representing the largest group of analytes that have been analyzed from cells by a single MSI study. In highly invasive cell lines, 31 lipids including phosphatidylglycerol (PG) and phosphatidic acids were found upregulated and eight lipids including sphingomyelin (SM) downregulated in negative ion mode. The products of de novo fatty acid synthesis incorporated into membrane phospholipids, like oleic-acid-containing PG, may be involved in mitochondrial dysfunction and thus affect the invasion of breast cancer cells. The deficiency of SM may be related to the disruption of apoptosis in highly invasive cancer cells. This work uncovered more analytes in cells by MSI than previous reports, providing a better visualization and novel insights to advance our understanding of the relationship between rapid progression of breast cancer and lipid metabolism. The most altered lipids may aid the discovery of diagnostic markers and therapeutic targets of breast cancer. Copyright

  19. Identification of lipidomic markers of chronic 3,3',4,4',5-pentachlorobiphenyl (PCB 126) exposure in the male rat liver.

    Science.gov (United States)

    Kania-Korwel, Izabela; Wu, Xianai; Wang, Kai; Lehmler, Hans-Joachim

    2017-09-01

    Exposure to PCB 126, an environmentally relevant aryl hydrocarbon receptor agonist, is an environmental factor causing hepatic steatosis in rodent models; however, the lipidome of PCB 126-exposed rats has not been investigated in-depth. The objective of the present study was therefore to characterize dose-dependent changes in the lipid profile in the liver of male Sprague-Dawley rats exposed to PCB 126. Rats were exposed for three month to intraperitoneal injections of 0.01, 0.05 and 0.2μmol/kg bw PCB 126 in corn oil. Control animals were exposed in parallel and received corn oil alone. Lipids were extracted from whole liver homogenate and levels of polar lipids and fatty acids incorporated into triglycerides (FA TAGs ) were determined with tandem mass spectrometry using electrospray ionization. PCB 126 exposure increased the hepatic content of polar lipids and FA TAGs . Protein adjusted levels of several polar lipid classes, in particular phosphatidylserine levels, decreased, whereas FA TAGs levels typically increased with increasing PCB 126 dose. Sensitive, dose-dependent endpoints of PCB 126 exposure included an increase in levels of adrenic acid incorporated into triglycerides and changes in levels of certain ether-linked phospholipid and 1-alkyl/1-alkenyldiacylglycerol species, as determined using partial least square discriminant analysis (PLS-DA) and ANOVA. These changes in the composition of polar lipids and fatty acid in the liver of PCB 126 exposed rats identified several novel markers of PCB 126-mediated fatty liver disease that need to be validated in further studies. Copyright © 2017 Elsevier B.V. All rights reserved.

  20. Maternal protein restriction during lactation induces early and lasting plasma metabolomic and hepatic lipidomic signatures of the offspring in a rodent programming model.

    Science.gov (United States)

    Martin Agnoux, Aurore; El Ghaziri, Angélina; Moyon, Thomas; Pagniez, Anthony; David, Agnès; Simard, Gilles; Parnet, Patricia; Qannari, El Mostafa; Darmaun, Dominique; Antignac, Jean-Philippe; Alexandre-Gouabau, Marie-Cécile

    2018-05-01

    Perinatal undernutrition affects not only fetal and neonatal growth but also adult health outcome, as suggested by the metabolic imprinting concept. However, the exact mechanisms underlying offspring metabolic adaptations are not yet fully understood. Specifically, it remains unclear whether the gestation or the lactation is the more vulnerable period to modify offspring metabolic flexibility. We investigated in a rodent model of intrauterine growth restriction (IUGR) induced by maternal protein restriction (R) during gestation which time window of maternal undernutrition (gestation, lactation or gestation-lactation) has more impact on the male offspring metabolomics phenotype. Plasma metabolome and hepatic lipidome of offspring were characterized through suckling period and at adulthood using liquid chromatography-high-resolution mass spectrometry. Multivariate analysis of these fingerprints highlighted a persistent metabolomics signature in rats suckled by R dams, with a clear-cut discrimination from offspring fed by control (C) dams. Pups submitted to a nutritional switch at birth presented a metabolomics signature clearly distinct from that of pups nursed by dams maintained on a consistent perinatal diet. Control rats suckled by R dams presented transiently higher branched-chain amino acid (BCAA) oxidation during lactation besides increased fatty acid (FA) β-oxidation, associated with preserved insulin sensitivity and lesser fat accretion that persisted throughout their life. In contrast, IUGR rats displayed permanently impaired β-oxidation, associated to increased glucose or BCAA oxidation at adulthood, depending on the fact that pups experienced slow postnatal or catch-up growth, as suckled by R or C dams, respectively. Taken together, these findings provide evidence for a significant contribution of the lactation period in metabolic programming. Copyright © 2018 Elsevier Inc. All rights reserved.

  1. Membrane phospholipid composition may contribute to exceptional longevity of the naked mole-rat (Heterocephalus glaber): a comparative study using shotgun lipidomics.

    Science.gov (United States)

    Mitchell, Todd W; Buffenstein, Rochelle; Hulbert, A J

    2007-11-01

    Phospholipids containing highly polyunsaturated fatty acids are particularly prone to peroxidation and membrane composition may therefore influence longevity. Phospholipid molecules, in particular those containing docosahexaenoic acid (DHA), from the skeletal muscle, heart, liver and liver mitochondria were identified and quantified using mass-spectrometry shotgun lipidomics in two similar-sized rodents that show an approximately 9-fold difference in maximum lifespan. The naked mole rat is the longest-living rodent known with a maximum lifespan of >28 years. Total phospholipid distribution is similar in tissues of both species; DHA is only found in phosphatidylcholines (PC), phosphatidylethanolamines (PE) and phosphatidylserines (PS), and DHA is relatively more concentrated in PE than PC. Naked mole-rats have fewer molecular species of both PC and PE than do mice. DHA-containing phospholipids represent 27-57% of all phospholipids in mice but only 2-6% in naked mole-rats. Furthermore, while mice have small amounts of di-polyunsaturated PC and PE, these are lacking in naked mole-rats. Vinyl ether-linked phospholipids (plasmalogens) are higher in naked mole-rat tissues than in mice. The lower level of DHA-containing phospholipids suggests a lower susceptibility to peroxidative damage in membranes of naked mole-rats compared to mice. Whereas the high level of plasmalogens might enhance membrane antioxidant protection in naked mole-rats compared to mice. Both characteristics possibly contribute to the exceptional longevity of naked mole-rats and may indicate a special role for peroxisomes in this extended longevity.

  2. Coupled Transcriptome and Proteome Analysis of Human Lymphotropic Tumor Viruses: Insights on the Detection and Discovery of Viral Genes

    Energy Technology Data Exchange (ETDEWEB)

    Dresang, Lindsay R.; Teuton, Jeremy R.; Feng, Huichen; Jacobs, Jon M.; Camp, David G.; Purvine, Samuel O.; Gritsenko, Marina A.; Li, Zhihua; Smith, Richard D.; Sugden, Bill; Moore, Patrick S.; Chang, Yuan

    2011-12-20

    Kaposi's sarcoma-associated herpesvirus (KSHV) and Epstein-Barr virus (EBV) are related human tumor viruses that cause primary effusion lymphomas (PEL) and Burkitt's lymphomas (BL), respectively. Viral genes expressed in naturally-infected cancer cells contribute to disease pathogenesis; knowing which viral genes are expressed is critical in understanding how these viruses cause cancer. To evaluate the expression of viral genes, we used high-resolution separation and mass spectrometry coupled with custom tiling arrays to align the viral proteomes and transcriptomes of three PEL and two BL cell lines under latent and lytic culture conditions. Results The majority of viral genes were efficiently detected at the transcript and/or protein level on manipulating the viral life cycle. Overall the correlation of expressed viral proteins and transcripts was highly complementary in both validating and providing orthogonal data with latent/lytic viral gene expression. Our approach also identified novel viral genes in both KSHV and EBV, and extends viral genome annotation. Several previously uncharacterized genes were validated at both transcript and protein levels. Conclusions This systems biology approach coupling proteome and transcriptome measurements provides a comprehensive view of viral gene expression that could not have been attained using each methodology independently. Detection of viral proteins in combination with viral transcripts is a potentially powerful method for establishing virus-disease relationships.

  3. Principle considerations for the use of transcriptomics in doping research.

    Science.gov (United States)

    Neuberger, Elmo W I; Moser, Dirk A; Simon, Perikles

    2011-10-01

    Over the course of the past decade, technical progress has enabled scientists to investigate genome-wide RNA expression using microarray platforms. This transcriptomic approach represents a promising tool for the discovery of basic gene expression patterns and for identification of cellular signalling pathways under various conditions. Since doping substances have been shown to influence mRNA expression, it has been suggested that these changes can be detected by screening the blood transcriptome. In this review, we critically discuss the potential but also the pitfalls of this application as a tool in doping research. Transcriptomic approaches were considered to potentially provide researchers with a unique gene expression signature or with a specific biomarker for various physiological and pathophysiological conditions. Since transcriptomic approaches are considerably prone to biological and technical confounding factors that act on study subjects or samples, very strict guidelines for the use of transcriptomics in human study subjects have been developed. Typical field conditions associated with doping controls limit the feasibility of following these strict guidelines as there are too many variables counteracting a standardized procedure. After almost a decade of research using transcriptomic tools, it still remains a matter of future technological progress to identify the ultimate biomarker using technologies and/or methodologies that are sufficiently robust against typical biological and technical bias and that are valid in a court of law. Copyright © 2011 John Wiley & Sons, Ltd.

  4. PIVOT: platform for interactive analysis and visualization of transcriptomics data.

    Science.gov (United States)

    Zhu, Qin; Fisher, Stephen A; Dueck, Hannah; Middleton, Sarah; Khaladkar, Mugdha; Kim, Junhyong

    2018-01-05

    Many R packages have been developed for transcriptome analysis but their use often requires familiarity with R and integrating results of different packages requires scripts to wrangle the datatypes. Furthermore, exploratory data analyses often generate multiple derived datasets such as data subsets or data transformations, which can be difficult to track. Here we present PIVOT, an R-based platform that wraps open source transcriptome analysis packages with a uniform user interface and graphical data management that allows non-programmers to interactively explore transcriptomics data. PIVOT supports more than 40 popular open source packages for transcriptome analysis and provides an extensive set of tools for statistical data manipulations. A graph-based visual interface is used to represent the links between derived datasets, allowing easy tracking of data versions. PIVOT further supports automatic report generation, publication-quality plots, and program/data state saving, such that all analysis can be saved, shared and reproduced. PIVOT will allow researchers with broad background to easily access sophisticated transcriptome analysis tools and interactively explore transcriptome datasets.

  5. Publishing scientifically sound papers in Traditional and Complementary Medicine.

    Science.gov (United States)

    Isidoro, Ciro; Huang, Chia-Chi; Sheen, Lee-Yan

    2016-01-01

    Non-conventional medical practices that make use of dietary supplements, herbal extracts, physical manipulations, and other practices typically associated with folk and Traditional Medicine are increasingly becoming popular in Western Countries. These practices are commonly referred to by the generic, all-inclusive term "Complementary and Alternative Medicine." Scientists, practitioners, and medical institutions bear the responsibility of testing and proving the effectiveness of these non-conventional medical practices in the interest of patients. In this context, the number of peer-reviewed journals and published articles on this topic has greatly increased in the recent decades. In this editorial article, we illustrate the policy of the Journal of Traditional and Complementary Medicine for publishing solid and scientifically sound papers in the field of Traditional and Complementary Medicine.

  6. JNC's experience of complementary accesses provided by the additional protocol

    International Nuclear Information System (INIS)

    Miura, Yasushi

    2001-01-01

    JNC (Japan Nuclear Cycle Development Institute) examined problems on implementation of the Additional Protocol to Japan/IAEA Safeguards Agreement with the Government of Japan and International Atomic Energy Agency through trials performed at Oarai Engineering Center before it entered into force. On December 16th 1999, the Additional Protocol entered into force, and in last January JNC provided the first JNC site information to STA. Then our Government provided it of all Japan to IAEA in last June. Also in this January, we sent the additional information changed from old one to MEXT (Ministry of Education, Culture, Sports, Science and Technology). The first Complementary Access of not only JNC but also Japan was implemented on JNC Ningyo-Toge Environmental Engineering Center on the end of last November. Since then, we have had over 10 times experience of Complementary Accesses for about one year especially on Tokai works and Ningyo-Toge. JNC's experience of Complementary Accesses will be introduced. (author)

  7. Complementary feeding: a commentary by the ESPGHAN Committee on Nutrition.

    Science.gov (United States)

    Agostoni, Carlo; Decsi, Tamas; Fewtrell, Mary; Goulet, Olivier; Kolacek, Sanja; Koletzko, Berthold; Michaelsen, Kim Fleischer; Moreno, Luis; Puntis, John; Rigo, Jacques; Shamir, Raanan; Szajewska, Hania; Turck, Dominique; van Goudoever, Johannes

    2008-01-01

    This position paper on complementary feeding summarizes evidence for health effects of complementary foods. It focuses on healthy infants in Europe. After reviewing current knowledge and practices, we have formulated these conclusions: Exclusive or full breast-feeding for about 6 months is a desirable goal. Complementary feeding (ie, solid foods and liquids other than breast milk or infant formula and follow-on formula) should not be introduced before 17 weeks and not later than 26 weeks. There is no convincing scientific evidence that avoidance or delayed introduction of potentially allergenic foods, such as fish and eggs, reduces allergies, either in infants considered at increased risk for the development of allergy or in those not considered to be at increased risk. During the complementary feeding period, >90% of the iron requirements of a breast-fed infant must be met by complementary foods, which should provide sufficient bioavailable iron. Cow's milk is a poor source of iron and should not be used as the main drink before 12 months, although small volumes may be added to complementary foods. It is prudent to avoid both early (or=7 months) introduction of gluten, and to introduce gluten gradually while the infant is still breast-fed, inasmuch as this may reduce the risk of celiac disease, type 1 diabetes mellitus, and wheat allergy. Infants and young children receiving a vegetarian diet should receive a sufficient amount ( approximately 500 mL) of breast milk or formula and dairy products. Infants and young children should not be fed a vegan diet.

  8. Optimal advertising and pricing decisions for complementary products

    Science.gov (United States)

    Taleizadeh, Ata Allah; Charmchi, Masoud

    2015-03-01

    Cooperative advertising is an agreement between a manufacturer and a retailer to share advertising cost at the local level. Previous studies have not investigated cooperative advertising for complementary products and their main focus was only on one good. In this paper, we study a two-echelon supply chain consisting of one manufacturer and one retailer with two complementary goods. The demand of each good is influenced not only by its price but also by the price of the other product. We use two game theory approaches to model this problem; Stackelberg manufacturer and Stackelberg retailer.

  9. Research methods in complementary and alternative medicine: an integrative review.

    Science.gov (United States)

    de Almeida Andrade, Fabiana; Schlechta Portella, Caio Fabio

    2018-01-01

    The scientific literature presents a modest amount of evidence in the use of complementary and alternative medicine (CAM). On the other hand, in practice, relevant results are common. The debates among CAM practitioners about the quality and execution of scientific research are important. Therefore, the aim of this review is to gather, synthesize and describe the differentiated methodological models that encompass the complexity of therapeutic interventions. The process of bringing evidence-based medicine into clinical practice in CAM is essential for the growth and strengthening of complementary medicines worldwide. Copyright © 2017 Shanghai Changhai Hospital. Published by Elsevier B.V. All rights reserved.

  10. Complementary and alternative medications for chronic pelvic pain.

    Science.gov (United States)

    Leong, Fah Che

    2014-09-01

    Chronic pelvic pain is common, but rarely cured, thus patients seek both second opinions and alternative means of controlling their pain. Complementary and alternative medicine accounts for 11.2% of out-of-pocket medical expenditures for adults for all conditions in the United States. Although there are many treatments, rigorous testing and well-done randomized studies are lacking. Dietary changes and physical modalities such as physical therapy have often been included in the category of alternative medicine, but their use is now considered mainstream. This article concentrates on other sources of alternative and complementary medicine, such as dietary supplementation and acupuncture. Copyright © 2014 Elsevier Inc. All rights reserved.

  11. Sequencing and characterization of the guppy (Poecilia reticulata transcriptome

    Directory of Open Access Journals (Sweden)

    Rodd F Helen

    2011-04-01

    Full Text Available Abstract Background Next-generation sequencing is providing researchers with a relatively fast and affordable option for developing genomic resources for organisms that are not among the traditional genetic models. Here we present a de novo assembly of the guppy (Poecilia reticulata transcriptome using 454 sequence reads, and we evaluate potential uses of this transcriptome, including detection of sex-specific transcripts and deployment as a reference for gene expression analysis in guppies and a related species. Guppies have been model organisms in ecology, evolutionary biology, and animal behaviour for over 100 years. An annotated transcriptome and other genomic tools will facilitate understanding the genetic and molecular bases of adaptation and variation in a vertebrate species with a uniquely well known natural history. Results We generated approximately 336 Mbp of mRNA sequence data from male brain, male body, female brain, and female body. The resulting 1,162,670 reads assembled into 54,921 contigs, creating a reference transcriptome for the guppy with an average read depth of 28×. We annotated nearly 40% of this reference transcriptome by searching protein and gene ontology databases. Using this annotated transcriptome database, we identified candidate genes of interest to the guppy research community, putative single nucleotide polymorphisms (SNPs, and male-specific expressed genes. We also showed that our reference transcriptome can be used for RNA-sequencing-based analysis of differential gene expression. We identified transcripts that, in juveniles, are regulated differently in the presence and absence of an important predator, Rivulus hartii, including two genes implicated in stress response. For each sample in the RNA-seq study, >50% of high-quality reads mapped to unique sequences in the reference database with high confidence. In addition, we evaluated the use of the guppy reference transcriptome for gene expression analyses in

  12. Complementary, Alternative, or Integrative Health: What's In a Name?

    Science.gov (United States)

    ... Information © Jupiter Images We’ve all seen the words “complementary,” “alternative,” and “ integrative ,” but what do they really mean? This fact sheet looks into these terms to help you understand them better and gives you a brief picture of NCCIH’s mission and role in this area ...

  13. Functions of Turkish complementary schools in the UK: Official vs ...

    African Journals Online (AJOL)

    This study focuses on one such Turkish complementary school in .... various educational services that lead to achieving certain goals .... languages, together with the issue of differences of quality of .... challenge of “tackling underachievement” of Turkish Speaking ..... Cape schools and implications for school leadership.

  14. Willingness to Pay for Complementary Health Care Insurance in Iran.

    Science.gov (United States)

    Nosratnejad, Shirin; Rashidian, Arash; Akbari Sari, Ali; Moradi, Najme

    2017-09-01

    Complementary health insurance is increasingly used to remedy the limitations and shortcomings of the basic health insurance benefit packages. Hence, it is essential to gather reliable information about the amount of Willingness to Pay (WTP) for health insurance. We assessed the WTP for health insurance in Iran in order to suggest an affordable complementary health insurance. The study sample consisted of 300 household heads all over provinces of Iran in 2013. The method applied was double bounded dichotomous choice and open-ended question approach of contingent valuation. The average WTP for complementary health insurance per person per month by double bounded dichotomous choice and open-ended question method respectively was 199000 and 115300 Rials (8 and 4.6 USD, respectively). Household's heads with higher levels of income and those who worked had more WTP for the health insurance. Besides, the WTP increased in direct proportion to the number of insured members of each household and in inverse proportion to the family size. The WTP value can be used as a premium in a society. As an important finding, the study indicated that the households were willing to pay higher premiums than currently collected for the complementary health insurance coverage in Iran. This offers the policy makers the opportunity to increase the premium and provide good benefits package for insured people of country then better risk pooling.

  15. Complementary Feeding Pattern in a Population of Pre-school ...

    African Journals Online (AJOL)

    Objective: It has been postulated that offering bland diets to infants could habituate to food refusal during early childhood. To investigate the complementary feeding pattern in Nigerian preschool children and a possible association with their current feeding habits, a cross-sectional study of two hundred (200) children was ...

  16. Optical Associative Memory Model With Threshold Modification Using Complementary Vector

    Science.gov (United States)

    Bian, Shaoping; Xu, Kebin; Hong, Jing

    1989-02-01

    A new criterion to evaluate the similarity between two vectors in associative memory is presented. According to it, an experimental research about optical associative memory model with threshold modification using complementary vector is carried out. This model is capable of eliminating the posibility to recall erroneously. Therefore the accuracy of reading out is improved.

  17. Nutritional and functional properties of a complementary food based ...

    African Journals Online (AJOL)

    The objective of this study was to determine the nutritional and functional properties of Amaranthus cruentus grain grown in Kenya for preparation of a ready-to-eat product that can be recommended as infant complementary food. Amaranth grains were subjected to steeping and steam pre-gelatinization to produce a ...

  18. Uniform and Complementary Social Interaction: Distinct Pathways to Solidarity.

    Science.gov (United States)

    Koudenburg, Namkje; Postmes, Tom; Gordijn, Ernestine H; van Mourik Broekman, Aafke

    2015-01-01

    We examine how different forms of co-action give rise to feelings of solidarity. We propose that (a) coordinated action elicits a sense of solidarity, and (b) the process through which such solidarity emerges differs for different forms of co-action. We suggest that whether solidarity within groups emerges from uniform action (e.g. synchronizing, as when people speak in unison) or from more complementary forms of action (e.g. alternating, when speaking in turns) has important consequences for the emergent position of individuals within the group. Uniform action relies on commonality, leaving little scope for individuality. In complementary action each individual makes a distinctive contribution to the group, thereby increasing a sense of personal value to the group, which should contribute to the emergence of solidarity. The predictions receive support from five studies, in which we study groups in laboratory and field settings. Results show that both complementary and uniform co-action increase a sense of solidarity compared to control conditions. However, in the complementary action condition, but not in the uniform action (or synchrony) condition, the effect on feelings of solidarity is mediated by a sense of personal value to the group.

  19. Complementary and alternative therapies for low back pain

    NARCIS (Netherlands)

    van Tulder, M.; Furlan, A.D.; Gagnier, J.J.

    2005-01-01

    The support for the principles of evidence-based medicine has increased within the field of complementary and alternative medicine (CAM). The objective of this chapter is to determine the effectiveness of CAM therapies compared to placebo, no intervention, or other interventions for acute/subacute

  20. Complementary and Alternative Therapies: An Evidence-Based Framework

    Science.gov (United States)

    Shaw, Steven R.

    2008-01-01

    Complementary and alternative medicine (CAM) has experienced a dramatic growth in use and acceptability over the last 20 years. CAM is a diverse collection of medical and healthcare systems, practices, and products that are not presently considered a component of conventional medicine. CAM traditionally has been practiced by informally educated…

  1. Governance and sustainability of the Argentine Complementary Currency Systems

    NARCIS (Netherlands)

    G.M. Gómez (Georgina)

    2012-01-01

    textabstractThe Redes de Trueque (RT) thrived during the economic crisis of 2001 – 2002 in Argentina and still stand out as one of the largest Complementary Currency System in the world. These local exchange networks reach a large scale during times of severe economic distress, but as large

  2. The scientific basis of alternative and complementary intervention in ...

    African Journals Online (AJOL)

    It is noted that some complementary treatment methods are not pharmacological in nature but employs natural forces, which are energy of some sorts. From the mass-energy equivalence known to orthodox science it is easy to conclude that every matter is crystallized energy and therefore all that exists in nature is energy in ...

  3. Complementary terrain/single beacon-based AUV navigation

    Digital Repository Service at National Institute of Oceanography (India)

    Maurya, P.; Curado, T.F.; António, P.

    is not sufficiently "rich" in terms of topographic features. The key contribution of this paper is a formal analysis of the benefits of using complementary filtering, in opposition to TAN navigation only. To this effect, we exploit key tools of estimation theory...

  4. Asouzu's Complementary Ontology as a Foundation for a Viable ...

    African Journals Online (AJOL)

    This paper on “Asouzu's Complementary Ontology as a foundation for a viable Ethic of the Environment”, posits that an ethic of the environment can be seen as viable if it considers the whole of reality as ontologically relevant. This point of view would free environmental ethics of anthropocentric bias and its attendant ...

  5. Reflections on Working Memory: Are the Two Models Complementary?

    Science.gov (United States)

    Pascual-Leone, Juan

    2000-01-01

    Compares and contrasts working memory theory of Baddeley and theory of constructive operators of Pascual- Leone. Concludes that although the theory of constructive operators is complementary with working memory theory (explains developmental and individual differences that working memory theory cannot), the converse is not true; theory of…

  6. Nutrient content and acceptability of soybean based complementary ...

    African Journals Online (AJOL)

    Nutrient content and acceptability of soybean based complementary food. ... African Journal of Food, Agriculture, Nutrition and Development ... A study was carried out in Morogoro region, Tanzania, to determine composition and acceptability of soy-based formulations with banana and cowpeas as traditional staples.

  7. [Complementary and alternative medicine: use in Montes Claros, Minas Gerais].

    Science.gov (United States)

    Neto, Joao Felício Rodrigues; Faria, Anderson Antônio de; Figueiredo, Maria Fernanda Santos

    2009-01-01

    To determine prevalence of utilization and social and economic profile of those using complementary and alternative medicine in the medium sized Brazilian city of Montes Claros, MG. A transversal descriptive study was conducted. The sample of 3090 people was probabilistic, by clusters using the household as the sample unit for interview of both genders, older than 18 years. Data were collected by semi-structured questionnaires. Utilization of complementary and alternative medicine was of 8.9% when only those involving costs such as homeopathy, acupuncture, chiropractics, techniques of relaxation/ meditation and massage are considered and of 70.0%, when all therapies found were included. Prevalent were prayers to God (52.0%), popular medicines (30.9%), physical exercises (25.5%), faith healers (15.0%), popular diets (7.1%), massage (4.9%), relaxation/meditation (2.8%), homeopathy (2.4%), and groups of self-help (1.9%), chiropractics (1.7%), acupuncture (1.5%) and orthomolecular medicine (0.2%). Women, Catholic, married of higher income and education were positively associated with utilization of therapies involving expenses. Complementary and alternative medicine is used by a significant number of those interviewed. Gender, religion, marital status, income and education were positively associated with utilization of complementary and alternative medicine. Access of those with less income and education could increase the utilization of the options that involve expenses.

  8. Functions of Turkish complementary schools in the UK: Official vs ...

    African Journals Online (AJOL)

    Complementary schools in the United Kingdom (UK) are community organised schools with the general aim of teaching younger generations their 'native' languages and cultures. However, the aims and practices of these schools are predominantly dependent on changes in the social and political contexts both in the host ...

  9. Uniform and Complementary Social Interaction: Distinct Pathways to Social Unity.

    NARCIS (Netherlands)

    Koudenburg, Namkje; Postmes, Tom; Gordijn, Ernestine; van Mourik Broekman, Aafke

    We examine how different forms of co-action (uniform vs. complementary co-action) give rise to feelings of solidarity. Five studies reveal that both forms of co-action increase solidarity, but have different consequences for the role of the individual within the group.

  10. Child factors associated with complementary feeding practices in ...

    African Journals Online (AJOL)

    Objectives: The objective of the study was to identify child factors that influenced complementary feeding practices in 2006 and 2011 in Uganda. Design: Trend analysis of Uganda Demographic and Health Surveys (UDHS) from 2006 and 2011. Subjects and setting: Children aged 6 to 23 months, Uganda. Results: Between ...

  11. Infant Feeding Practices and the Effect of Early Complementary ...

    African Journals Online (AJOL)

    Objective: The objective of this study was to determine infant feeding practices and the effect of early complementary feeding on the nutritional status of children in Makada Community, Sabon Gari Local Government Area (LGA), Kaduna State, Nigeria. Materials and Methods: A cross-sectional survey was carried out.

  12. Developing a Culture of Readers: Complementary Materials That Engage

    Science.gov (United States)

    Sailors, Misty; Kaambankadzanja, Davie

    2017-01-01

    Many professionals, including members of the International Literacy Association, are concerned with the lack of reading materials in classrooms across the world. In this paper, the authors present the creation of high-quality, locally produced, complementary reading materials in Malawi, where there are very few children's books and few…

  13. Complementary and Alternative Medicine: Core Competencies for Family Nurse Practitioners.

    Science.gov (United States)

    Burman, Mary E.

    2003-01-01

    Directors of family nurse practitioner education programs (n=141) reported inclusion of some complementary/alternative medicine content (CAM), most commonly interviewing patients about CAM, critical thinking, evidence-based medicine, laws, ethics, and spiritual/cultural beliefs. Definition of CAM was medically, not holistically based. More faculty…

  14. Information Discovery from Complementary Literatures: Categorizing Viruses as Potential Weapons.

    Science.gov (United States)

    Swanson, Don R.; Smalheiser, Neil R.; Bookstein, A.

    2001-01-01

    This project demonstrates how techniques of analyzing complementary literatures might be applied to problems of defense against biological weapons. The article is based solely on the open-source scientific literature, and is oriented on informatics techniques. Findings are intended as a guide to the virus literature to support further studies that…

  15. The Financing of Complementary Currencies: Problems and Perspectives

    NARCIS (Netherlands)

    R.F.H. Schroeder (Rolf)

    2015-01-01

    textabstractCosts and cost coverage of complementary currencies has been neglected by researchers so far. This article provides an analysis of the different types of costs incurred and asks for appropriate means of financing such projects. External public and private sources are discussed in a

  16. Selection of complementary foods based on optimal nutritional values

    DEFF Research Database (Denmark)

    Sen, Partho; Mardinogulu, Adil; Nielsen, Jens

    2017-01-01

    Human milk is beneficial for growth and development of infants. Several factors result in mothers ceasing breastfeeding which leads to introduction of breast-milk substitutes (BMS). In some communities traditional foods are given as BMS, in others they are given as complementary foods during...

  17. Antiretrovirals and the use of traditional, complementary and ...

    African Journals Online (AJOL)

    The aim of this prospective study (20 months) was to assess HIV patients' use of Traditional, Complementary and Alternative Medicine (TCAM) and its effect on ARV adherence at three public hospitals in KwaZulu-Natal, South Africa. Seven hundred and thirty-five (29.8% male and 70.2% female) patients who consecutively ...

  18. The usage of complementary and alternative medicine in ...

    African Journals Online (AJOL)

    Introduction: the use of complementary and alternative medicine (CAM) has increased over the last few years, and an emergent data suggests that some CAM modalities may be helpful in addressing gastrointestinal (GI) conditions. Our aimwas to find out the prevalence ofsuch practices for GI condition amongst patients ...

  19. Complementary Alternative Medicine for Children with Autism: A Physician Survey

    Science.gov (United States)

    Golnik, Allison E.; Ireland, Marjorie

    2009-01-01

    Previous studies suggest over half of children with autism are using complementary alternative medicine (CAM). In this study, physicians responded (n = 539, 19% response rate) to a survey regarding CAM use in children with autism. Physicians encouraged multi-vitamins (49%), essential fatty acids (25%), melatonin (25%) and probiotics (19%) and…

  20. Determinants of public trust in complementary and alternative medicine

    NARCIS (Netherlands)

    Schee, E. van der; Groenewegen, P.P.

    2010-01-01

    Background: In the Netherlands, public trust in conventional medicine is relatively high. There is reason to believe that public trust in complementary and alternative medicine (CAM) is rated lower. The aim of this study is to gain insight into public trust in CAM and the determinants that lie at

  1. Complementary medicine use among Moroccan patients with cancer

    African Journals Online (AJOL)

    Background: Complementary and alternative medicine (CAM) is a group of diverse medical and health care systems, practices, and products that are not generally considered part of conventional medicine. As cancer incidence rates and survival time increase, use of CAM will likely increase. However, little is known about ...

  2. Interest in and Willingness to Use Complementary, Alternative and ...

    African Journals Online (AJOL)

    Background: Healthcare systems worldwide are changing and the use of complementary, alternative and traditional medicine (CAM) form part of this transformation. South Africa has a large number of CAM practitioners, but they are not included in the official healthcare system. The aim of this study was to determine the ...

  3. Use of complementary and alternative medicine by cancer patients ...

    African Journals Online (AJOL)

    Complementary and alternative medicine (CAM) is garnering increasing interest and acceptance among the general population throughout the world. The use of CAM by cancer patients is very common in China. The referenced English literature has no rural community-based study from China on this subject. This study ...

  4. An insight into the use of complementary and alternative medicines ...

    African Journals Online (AJOL)

    Background: Complementary and alternative medicines (CAM) are increasingly popular globally with frequent use amongst patients with atopic eczema (AE). Despite increased AE prevalence in South Africa (SA), no local data on CAM-use for this disease exists. Methods: A cross-sectional study utilizing a comprehensive ...

  5. The Problem of Complementary and Alternative Medicine Use Today

    DEFF Research Database (Denmark)

    MacArtney, John; Wahlberg, Ayo

    2014-01-01

    Commentators like Goldacre, Dawkins, and Singh and Ernst are worried that the rise in complementary and alternative medicine (CAM) represents a flight from science propagated by enemies of reason. We outline what kind of problem CAM use is for these commentators and find that users of CAM...

  6. Assessment of the Essential and Toxic Elements in Complementary ...

    African Journals Online (AJOL)

    In this study, the commonly used complementary foods (Unga wa Lishe) for children 0-5 years in Tanzania were analyze for essential and toxic elements in order to assess their nutritional levels. 60 samples were purchased from shops in Dar es Salaam, Moshi and Arusha regions and analyzed using Energy Dispersive ...

  7. Complementary and alternative therapies for back pain II.

    NARCIS (Netherlands)

    Furlan, Andrea D.; Yazdi, Fatemeh; Tsertsvadze, Alexander; Gross, Anita; Van Tulder, Maurits; Santaguida, Lina; Cherkin, Dan; Gagnier, Joel J.; Ammendolia, Carlo; Ansari, Mohammed T.; Ostermann, Thomas; Dryden, Trish; Doucette, Steve; Skidmore, Becky; Daniel, Raymond; Tsouros, Sophia; Weeks, Laura; Galipeau, James

    2010-01-01

    Back and neck pain are important health problems with serious societal and economic implications. Conventional treatments have been shown to have limited benefit in improving patient outcomes. Complementary and Alternative Medicine (CAM) therapies offer additional options in the management of low

  8. Complementary Health Approaches for Smoking Cessation: What the Science Says

    Science.gov (United States)

    ... health professionals Complementary Health Approaches for Smoking Cessation: What the Science Says Share: November 2017 Mind and Body Practices ... as a smoking cessation treatment, authorizing Achieve Life Science, Inc. to proceed with clinical ... What Does the Research Show? A 2016 Cochrane review ...

  9. Technological aspects of preparing affordable fermented complementary foods.

    NARCIS (Netherlands)

    Nout, M.J.R.; Ngoddy, P.O.

    1997-01-01

    The requirements and manufacturing procedure of complementary (weaning) foods is discussed. Nutritional requirements for infants (aged 6-12 months) include approx. 3 MJ energy and 14 g digestible protein per litre, of a semi-liquid porridge. Microbiological safety is enhanced by biological

  10. Midwives' support for Complementary and Alternative Medicine: a literature review.

    Science.gov (United States)

    Hall, Helen G; McKenna, Lisa G; Griffiths, Debra L

    2012-03-01

    There is evidence that the use of Complementary and Alternative Medicine by childbearing women is becoming increasingly popular in industrialised countries. The aim of this is paper is to review the research literature investigating the midwives' support for the use of these therapies. A search for relevant research published from 2000 to 2009 was undertaken using a range of databases and by examining relevant bibliographies. A total of thirteen studies were selected for inclusion in this review. The findings indicate that the use of Complementary and Alternative Medicine is widespread in midwifery practice. Common indications for use include; labour induction and augmentation, nausea and vomiting, relaxation, back pain, anaemia, mal-presentation, perineal discomfort, postnatal depression and lactation problems. The most popular therapies recommended by midwives are massage therapy, herbal medicines, relaxation techniques, nutritional supplements, aromatherapy, homeopathy and acupuncture. Midwives support the use Complementary and Alternative Medicine because they believe it is philosophically congruent; it provides safe alternatives to medical interventions; it supports the woman's autonomy, and; incorporating Complementary and Alternative Medicine can enhance their own professional autonomy. There is considerable support by midwives for the use of Complementary and Alternative Medicine by expectant women. Despite this enthusiasm, currently there are few educational opportunities and only limited research evidence regarding CAM use in midwifery practice. These shortfalls need to be addressed by the profession. Midwives are encouraged to have an open dialogue with childbearing women, to document use and to base any advice on the best available evidence. Copyright © 2010 Australian College of Midwives. Published by Elsevier Ltd. All rights reserved.

  11. [Obesity and complementary feeding time: a period at risk].

    Science.gov (United States)

    Vidailhet, M

    2010-12-01

    Relation between rapid growth during the first months of life and secondary risk of excessive adiposity is well demonstrated. Many works have indicated a birth feeding effect on weight gain during the first year of life and a protective effect towards later childhood and adult obesity. However all these studies are observational and several works denied this protective effect. Concerning complementary feeding, 3 interventional, randomized, studies achieved between 4 and 6 months of age, showed a good regulation of caloric intake and no weight gain modification due to complementary foods. Most of others studies are observational and don't show any relation between time of introduction of complementary foods and later fat mass. However 3 recent studies indicate, respectively at 7, 10 and 42 years of age, an increased adiposity, suggesting the possibility of a programmed excessive fat gain induced by an early complementary foods introduction. Very few studies have evaluated, besides the time of weaning, the kind, quantity and caloric density of foods used as complements, whereas other recent studies show the importance of appetite differences since the first months of life and the importance of genetic influence on these variations. Others works have emphasized the possible role of an excessive protein intake during the first 2 years of life. So, it appears that it may be necessary to pay attention not only on the date, but also on the kind and quantity of complementary foods, particularly in infants at risk for obesity, because of parental obesity, rapid weight growth or an excessive appetite. Copyright © 2010 Elsevier Masson SAS. All rights reserved.

  12. Self-complementary circular codes in coding theory.

    Science.gov (United States)

    Fimmel, Elena; Michel, Christian J; Starman, Martin; Strüngmann, Lutz

    2018-04-01

    Self-complementary circular codes are involved in pairing genetic processes. A maximal [Formula: see text] self-complementary circular code X of trinucleotides was identified in genes of bacteria, archaea, eukaryotes, plasmids and viruses (Michel in Life 7(20):1-16 2017, J Theor Biol 380:156-177, 2015; Arquès and Michel in J Theor Biol 182:45-58 1996). In this paper, self-complementary circular codes are investigated using the graph theory approach recently formulated in Fimmel et al. (Philos Trans R Soc A 374:20150058, 2016). A directed graph [Formula: see text] associated with any code X mirrors the properties of the code. In the present paper, we demonstrate a necessary condition for the self-complementarity of an arbitrary code X in terms of the graph theory. The same condition has been proven to be sufficient for codes which are circular and of large size [Formula: see text] trinucleotides, in particular for maximal circular codes ([Formula: see text] trinucleotides). For codes of small-size [Formula: see text] trinucleotides, some very rare counterexamples have been constructed. Furthermore, the length and the structure of the longest paths in the graphs associated with the self-complementary circular codes are investigated. It has been proven that the longest paths in such graphs determine the reading frame for the self-complementary circular codes. By applying this result, the reading frame in any arbitrary sequence of trinucleotides is retrieved after at most 15 nucleotides, i.e., 5 consecutive trinucleotides, from the circular code X identified in genes. Thus, an X motif of a length of at least 15 nucleotides in an arbitrary sequence of trinucleotides (not necessarily all of them belonging to X) uniquely defines the reading (correct) frame, an important criterion for analyzing the X motifs in genes in the future.

  13. Network Analysis of Rodent Transcriptomes in Spaceflight

    Science.gov (United States)

    Ramachandran, Maya; Fogle, Homer; Costes, Sylvain

    2017-01-01

    Network analysis methods leverage prior knowledge of cellular systems and the statistical and conceptual relationships between analyte measurements to determine gene connectivity. Correlation and conditional metrics are used to infer a network topology and provide a systems-level context for cellular responses. Integration across multiple experimental conditions and omics domains can reveal the regulatory mechanisms that underlie gene expression. GeneLab has assembled rich multi-omic (transcriptomics, proteomics, epigenomics, and epitranscriptomics) datasets for multiple murine tissues from the Rodent Research 1 (RR-1) experiment. RR-1 assesses the impact of 37 days of spaceflight on gene expression across a variety of tissue types, such as adrenal glands, quadriceps, gastrocnemius, tibalius anterior, extensor digitorum longus, soleus, eye, and kidney. Network analysis is particularly useful for RR-1 -omics datasets because it reinforces subtle relationships that may be overlooked in isolated analyses and subdues confounding factors. Our objective is to use network analysis to determine potential target nodes for therapeutic intervention and identify similarities with existing disease models. Multiple network algorithms are used for a higher confidence consensus.

  14. Transcriptomic analysis of Salmonella desiccation resistance.

    Science.gov (United States)

    Li, Haiping; Bhaskara, Anuhya; Megalis, Christina; Tortorello, Mary Lou

    2012-12-01

    The survival of Salmonella in low moisture foods and processing environments remains a great challenge for the food industry and public health. To explore the mechanisms of Salmonella desiccation resistance, we studied the transcriptomic responses in Salmonella Tennessee (Tennessee), using Salmonella Typhimurium LT2 (LT2), a strain weakly resistant to desiccation, as a reference strain. In response to 2 h of air-drying at 11% equilibrated relative humidity, approximately one-fourth of the open reading frames (ORFs) in the Tennessee genome and one-fifth in LT2 were differentially expressed (>2-fold). Among all differentially expressed functional groups (>5-fold) in both strains, the expression fold change associated with fatty acid metabolism was the highest, and constituted 51% and 35% of the total expression fold change in Tennessee and LT2, respectively. Tennessee showed greater changes in expression of genes associated with stress response and envelope modification than LT2, while showing lesser changes in protein biosynthesis expression. Expression of flagella genes was significantly more inhibited in stationary phase cells of Tennessee than LT2 both before and after desiccation. The accumulation of the osmolyte trehalose was significantly induced by desiccation in Tennessee, but no increase was detectable in LT2, which is consistent with the expression patterns of the entire trehalose biosynthesis and degradation pathways in both strains. Results from this study present a global view of the dynamic desiccation responses in Salmonella, which will guide future research efforts to control Salmonella in low moisture environments.

  15. A transcriptome approach to ecdysozoan phylogeny.

    Science.gov (United States)

    Borner, Janus; Rehm, Peter; Schill, Ralph O; Ebersberger, Ingo; Burmester, Thorsten

    2014-11-01

    The monophyly of Ecdysozoa, which comprise molting phyla, has received strong support from several lines of evidence. However, the internal relationships of Ecdysozoa are still contended. We generated expressed sequence tags from a priapulid (penis worm), a kinorhynch (mud dragon), a tardigrade (water bear) and five chelicerate taxa by 454 transcriptome sequencing. A multigene alignment was assembled from 63 taxa, which comprised after matrix optimization 24,249 amino acid positions with high data density (2.6% gaps, 19.1% missing data). Phylogenetic analyses employing various models support the monophyly of Ecdysozoa. A clade combining Priapulida and Kinorhyncha (i.e. Scalidophora) was recovered as the earliest branch among Ecdysozoa. We conclude that Cycloneuralia, a taxon erected to combine Priapulida, Kinorhyncha and Nematoda (and others), are paraphyletic. Rather Arthropoda (including Onychophora) are allied with Nematoda and Tardigrada. Within Arthropoda, we found strong support for most clades, including monophyletic Mandibulata and Pancrustacea. The phylogeny within the Euchelicerata remained largely unresolved. There is conflicting evidence on the position of tardigrades: While Bayesian and maximum likelihood analyses of only slowly evolving genes recovered Tardigrada as a sister group to Arthropoda, analyses of the full data set, and of subsets containing genes evolving at fast and intermediate rates identified a clade of Tardigrada and Nematoda. Notably, the latter topology is also supported by the analyses of indel patterns. Copyright © 2014 Elsevier Inc. All rights reserved.

  16. Gingival tissue transcriptomes in experimental gingivitis

    Science.gov (United States)

    Jönsson, Daniel; Ramberg, Per; Demmer, Ryan T.; Kebschull, Moritz; Dahlén, Gunnar; Papapanou, Panos N.

    2012-01-01

    Aims We investigated the sequential gene expression in the gingiva during the induction and resolution of experimental gingivitis. Methods Twenty periodontally and systemically healthy non-smoking volunteers participated in a 3-week experimental gingivitis protocol, followed by debridement and 2-week regular plaque control. We recorded clinical indices and harvested gingival tissue samples from 4 interproximal palatal sites in half of the participants at baseline, Day 7, 14 and 21 (‘induction phase’), and at day 21, 25, 30 and 35 in the other half (‘resolution phase’). RNA was extracted, amplified, reversed transcribed, amplified, labeled and hybridized with Affymetrix Human Genome U133Plus2.0 microarrays. Paired t-tests compared gene expression changes between consecutive time points. Gene ontology analyses summarized the expression patterns into biologically relevant categories. Results The median gingival index was 0 at baseline, 2 at Day 21 and 1 at Day 35. Differential gene regulation peaked during the third week of induction and the first four days of resolution. Leukocyte transmigration, cell adhesion and antigen processing/presentation were the top differentially regulated pathways. Conclusions Transcriptomic studies enhance our understanding of the pathobiology of the reversible inflammatory gingival lesion and provide a detailed account of the dynamic tissue responses during induction and resolution of experimental gingivitis. PMID:21501207

  17. Transcriptome analysis of zebrafish embryogenesis using microarrays.

    Directory of Open Access Journals (Sweden)

    Sinnakaruppan Mathavan

    2005-08-01

    Full Text Available Zebrafish (Danio rerio is a well-recognized model for the study of vertebrate developmental genetics, yet at the same time little is known about the transcriptional events that underlie zebrafish embryogenesis. Here we have employed microarray analysis to study the temporal activity of developmentally regulated genes during zebrafish embryogenesis. Transcriptome analysis at 12 different embryonic time points covering five different developmental stages (maternal, blastula, gastrula, segmentation, and pharyngula revealed a highly dynamic transcriptional profile. Hierarchical clustering, stage-specific clustering, and algorithms to detect onset and peak of gene expression revealed clearly demarcated transcript clusters with maximum gene activity at distinct developmental stages as well as co-regulated expression of gene groups involved in dedicated functions such as organogenesis. Our study also revealed a previously unidentified cohort of genes that are transcribed prior to the mid-blastula transition, a time point earlier than when the zygotic genome was traditionally thought to become active. Here we provide, for the first time to our knowledge, a comprehensive list of developmentally regulated zebrafish genes and their expression profiles during embryogenesis, including novel information on the temporal expression of several thousand previously uncharacterized genes. The expression data generated from this study are accessible to all interested scientists from our institute resource database (http://giscompute.gis.a-star.edu.sg/~govind/zebrafish/data_download.html.

  18. Transcriptome profiling of Elettaria cardamomum (L. Maton (small cardamom

    Directory of Open Access Journals (Sweden)

    F. Nadiya

    2017-03-01

    Full Text Available Elettaria cardamomum (L. Maton, known as ‘queen of spices, is a perennial herbaceous monocot of the family Zingiberaceae, native to southern India. Cardamom is an economically valuable spice crop and used widely in culinary and medicinal purposes. In the present study, using Ion Proton RNA sequencing technology, we performed transcriptome sequencing and de novo transcriptome assembly of a wild and five cultivar genotypes of cardamom. RNA-seq generated a total of 22,811,983 (92 base and 24,889,197 (75 base raw reads accounting for approximately 8.21GB and 7.65GB of sequence data for wild and cultivar genotypes of cardamom respectively. The raw data were submitted to SRA database of NCBI under the accession numbers SRX1141272 (wild and SRX1141276 (cultivars. The raw reads were quality filtered and assembled using MIRA assembler resulted with 112,208 and 264,161contigs having N50 value 616 and 664 for wild and cultivar cardamom respectively. The assembled unigenes were functionally annotated using several databases including PlantCyc for pathway annotation. This work represents the first report on cardamom transcriptome sequencing. In order to generate a comprehensive reference transcriptome, we further assembled the raw reads of wild and cultivar genotypes which might enrich the plant transcriptome database and trigger advanced research in cardamom genomics.

  19. Analysis of the Citrullus colocynthis transcriptome during water deficit stress.

    Directory of Open Access Journals (Sweden)

    Zhuoyu Wang

    Full Text Available Citrullus colocynthis is a very drought tolerant species, closely related to watermelon (C. lanatus var. lanatus, an economically important cucurbit crop. Drought is a threat to plant growth and development, and the discovery of drought inducible genes with various functions is of great importance. We used high throughput mRNA Illumina sequencing technology and bioinformatic strategies to analyze the C. colocynthis leaf transcriptome under drought treatment. Leaf samples at four different time points (0, 24, 36, or 48 hours of withholding water were used for RNA extraction and Illumina sequencing. qRT-PCR of several drought responsive genes was performed to confirm the accuracy of RNA sequencing. Leaf transcriptome analysis provided the first glimpse of the drought responsive transcriptome of this unique cucurbit species. A total of 5038 full-length cDNAs were detected, with 2545 genes showing significant changes during drought stress. Principle component analysis indicated that drought was the major contributing factor regulating transcriptome changes. Up regulation of many transcription factors, stress signaling factors, detoxification genes, and genes involved in phytohormone signaling and citrulline metabolism occurred under the water deficit conditions. The C. colocynthis transcriptome data highlight the activation of a large set of drought related genes in this species, thus providing a valuable resource for future functional analysis of candidate genes in defense of drought stress.

  20. Developmental Transcriptome for a Facultatively Eusocial Bee, Megalopta genalis.

    Science.gov (United States)

    Jones, Beryl M; Wcislo, William T; Robinson, Gene E

    2015-08-14

    Transcriptomes provide excellent foundational resources for mechanistic and evolutionary analyses of complex traits. We present a developmental transcriptome for the facultatively eusocial bee Megalopta genalis, which represents a potential transition point in the evolution of eusociality. A de novo transcriptome assembly of Megalopta genalis was generated using paired-end Illumina sequencing and the Trinity assembler. Males and females of all life stages were aligned to this transcriptome for analysis of gene expression profiles throughout development. Gene Ontology analysis indicates that stage-specific genes are involved in ion transport, cell-cell signaling, and metabolism. A number of distinct biological processes are upregulated in each life stage, and transitions between life stages involve shifts in dominant functional processes, including shifts from transcriptional regulation in embryos to metabolism in larvae, and increased lipid metabolism in adults. We expect that this transcriptome will provide a useful resource for future analyses to better understand the molecular basis of the evolution of eusociality and, more generally, phenotypic plasticity. Copyright © 2015 Jones et al.

  1. Evaluating de Bruijn graph assemblers on 454 transcriptomic data.

    Directory of Open Access Journals (Sweden)

    Xianwen Ren

    Full Text Available Next generation sequencing (NGS technologies have greatly changed the landscape of transcriptomic studies of non-model organisms. Since there is no reference genome available, de novo assembly methods play key roles in the analysis of these data sets. Because of the huge amount of data generated by NGS technologies for each run, many assemblers, e.g., ABySS, Velvet and Trinity, are developed based on a de Bruijn graph due to its time- and space-efficiency. However, most of these assemblers were developed initially for the Illumina/Solexa platform. The performance of these assemblers on 454 transcriptomic data is unknown. In this study, we evaluated and compared the relative performance of these de Bruijn graph based assemblers on both simulated and real 454 transcriptomic data. The results suggest that Trinity, the Illumina/Solexa-specialized transcriptomic assembler, performs the best among the multiple de Bruijn graph assemblers, comparable to or even outperforming the standard 454 assembler Newbler which is based on the overlap-layout-consensus algorithm. Our evaluation is expected to provide helpful guidance for researchers to choose assemblers when analyzing 454 transcriptomic data.

  2. Characterization of substrate preference for Slc1p and Cst26p in Saccharomyces cerevisiae using lipidomic approaches and an LPAAT activity assay.

    Directory of Open Access Journals (Sweden)

    Guanghou Shui

    Full Text Available BACKGROUND: Phosphatidic acid (PA is a key regulated intermediate and precursor for de novo biosynthesis of all glycerophospholipids. PA can be synthesized through the acylation of lysophosphatidic acid (LPA by 1-acyl-3-phosphate acyltransferase (also called lysophosphatidic acid acyltransferase, LPAAT. Recent findings have substantiated the essential roles of acyltransferases in various biological functions. METHODOLOGIES/PRINCIPAL FINDINGS: We used a flow-injection-based lipidomic approach with approximately 200 multiple reaction monitoring (MRM transitions to pre-screen fatty acyl composition of phospholipids in the yeast Saccharomyces cerevisiae mutants. Dramatic changes were observed in fatty acyl composition in some yeast mutants including Slc1p, a well-characterized LPAAT, and Cst26p, a recently characterized phosphatidylinositol stearoyl incorporating 1 protein and putative LPAAT in S. cerevisiae. A comprehensive high-performance liquid chromatography-based multi-stage MRM approach (more than 500 MRM transitions was developed and further applied to quantify individual phospholipids in both strains to confirm these changes. Our data suggest potential fatty acyl substrates as well as fatty acyls that compensate for defects in both Cst26p and Slc1p mutants. These results were consistent with those from a non-radioactive LPAAT enzymatic assay using C17-LPA and acyl-CoA donors as substrates. CONCLUSIONS: We found that Slc1p utilized fatty acid (FA 18:1 and FA 14:0 as substrates to synthesize corresponding PAs; moreover, it was probably the only acyltransferase responsible for acylation of saturated short-chain fatty acyls (12:0 and 10:0 in S. cerevisiae. We also identified FA 18:0, FA 16:0, FA 14:0 and exogenous FA 17:0 as preferred substrates for Cst26p because transformation with a GFP-tagged CST26 restored the phospholipid profile of a CST26 mutant. Our current findings expand the enzymes and existing scope of acyl-CoA donors for

  3. The testes transcriptome derived from the New World Screwworm, Cochliomyia hominivorax TSA

    Science.gov (United States)

    In a collaboration with National Center for Genome Resources researchers, we sequenced and assembled the testes transcriptome derived from the Pacora, Panama, production plant strain of the New World Screwworm, Cochliomyia hominivorax. This transcriptome contains 4,149 unigenes and the Transcriptome...

  4. Major differences between human atopic dermatitis and murine models as determined by global transcriptomic profiling

    DEFF Research Database (Denmark)

    Ewald, David Adrian; Noda, Shinji; Oliva, Margeaux

    2017-01-01

    , and a comparison of these models with the human AD transcriptomic fingerprint is lacking. We sought to evaluate the transcriptomic profiles of six common murine models and determine how they relate to human AD skin. Transcriptomic profiling was performed using microarrays and qRT-PCR on biopsies from NC/Nga, flaky...

  5. De novo transcriptome assembly of shrimp Palaemon serratus

    Directory of Open Access Journals (Sweden)

    Alejandra Perina

    2017-03-01

    Full Text Available The shrimp Palaemon serratus is a coastal decapod crustacean with a high commercial value. It is harvested for human consumption. In this study, we used Illumina sequencing technology (HiSeq 2000 to sequence, assemble and annotate the transcriptome of P. serratus. RNA was isolated from muscle of adults individuals and, from a pool of larvae. A total number of 4 cDNA libraries were constructed, using the TruSeq RNA Sample Preparation Kit v2. The raw data in this study was deposited in NCBI SRA database with study accession number of SRP090769. The obtained data were subjected to de novo transcriptome assembly using Trinity software, and coding regions were predicted by TransDecoder. We used Blastp and Sma3s to annotate the identified proteins. The transcriptome data could provide some insight into the understanding of genes involved in the larval development and metamorphosis.

  6. Transcriptomic signatures of ash (Fraxinus spp. phloem.

    Directory of Open Access Journals (Sweden)

    Xiaodong Bai

    2011-01-01

    Full Text Available Ash (Fraxinus spp. is a dominant tree species throughout urban and forested landscapes of North America (NA. The rapid invasion of NA by emerald ash borer (Agrilus planipennis, a wood-boring beetle endemic to Eastern Asia, has resulted in the death of millions of ash trees and threatens billions more. Larvae feed primarily on phloem tissue, which girdles and kills the tree. While NA ash species including black (F. nigra, green (F. pennsylvannica and white (F. americana are highly susceptible, the Asian species Manchurian ash (F. mandshurica is resistant to A. planipennis perhaps due to their co-evolutionary history. Little is known about the molecular genetics of ash. Hence, we undertook a functional genomics approach to identify the repertoire of genes expressed in ash phloem.Using 454 pyrosequencing we obtained 58,673 high quality ash sequences from pooled phloem samples of green, white, black, blue and Manchurian ash. Intriguingly, 45% of the deduced proteins were not significantly similar to any sequences in the GenBank non-redundant database. KEGG analysis of the ash sequences revealed a high occurrence of defense related genes. Expression analysis of early regulators potentially involved in plant defense (i.e. transcription factors, calcium dependent protein kinases and a lipoxygenase 3 revealed higher mRNA levels in resistant ash compared to susceptible ash species. Lastly, we predicted a total of 1,272 single nucleotide polymorphisms and 980 microsatellite loci, among which seven microsatellite loci showed polymorphism between different ash species.The current transcriptomic data provide an invaluable resource for understanding the genetic make-up of ash phloem, the target tissue of A. planipennis. These data along with future functional studies could lead to the identification/characterization of defense genes involved in resistance of ash to A. planipennis, and in future ash breeding programs for marker development.

  7. Complementary and alternative exercise for fibromyalgia: a meta-analysis

    Directory of Open Access Journals (Sweden)

    Mist SD

    2013-03-01

    Full Text Available Scott David Mist, Kari Firestone, Kim Dupree Jones Fibromyalgia Research and Treatment Group, School of Nursing, Oregon Health and Science University, Portland, OR, USA Abstract: Complementary and alternative medicine includes a number of exercise modalities, such as tai chi, qigong, yoga, and a variety of lesser-known movement therapies. A meta-analysis of the current literature was conducted estimating the effect size of the different modalities, study quality and bias, and adverse events. The level of research has been moderately weak to date, but most studies report a medium-to-high effect size in pain reduction. Given the lack of adverse events, there is little risk in recommending these modalities as a critical component in a multimodal treatment plan, which is often required for fibromyalgia management. Keywords: fibromyalgia, exercise, complementary and alternative, efficacy, safety

  8. Complementary Therapy for Addiction: “Drumming Out Drugs”

    Science.gov (United States)

    Winkelman, Michael

    2003-01-01

    Objectives. This article examines drumming activities as complementary addiction treatments and discusses their reported effects. Methods. I observed drumming circles for substance abuse (as a participant), interviewed counselors and Internet mailing list participants, initiated a pilot program, and reviewed literature on the effects of drumming. Results. Research reviews indicate that drumming enhances recovery through inducing relaxation and enhancing theta-wave production and brain-wave synchronization. Drumming produces pleasurable experiences, enhanced awareness of preconscious dynamics, release of emotional trauma, and reintegration of self. Drumming alleviates self-centeredness, isolation, and alienation, creating a sense of connectedness with self and others. Drumming provides a secular approach to accessing a higher power and applying spiritual perspectives. Conclusions. Drumming circles have applications as complementary addiction therapy, particularly for repeated relapse and when other counseling modalities have failed. PMID:12660212

  9. A molybdenum disulfide/carbon nanotube heterogeneous complementary inverter.

    Science.gov (United States)

    Huang, Jun; Somu, Sivasubramanian; Busnaina, Ahmed

    2012-08-24

    We report a simple, bottom-up/top-down approach for integrating drastically different nanoscale building blocks to form a heterogeneous complementary inverter circuit based on layered molybdenum disulfide and carbon nanotube (CNT) bundles. The fabricated CNT/MoS(2) inverter is composed of n-type molybdenum disulfide (MOS(2)) and p-type CNT transistors, with a high voltage gain of 1.3. The CNT channels are fabricated using directed assembly while the layered molybdenum disulfide channels are fabricated by mechanical exfoliation. This bottom-up fabrication approach for integrating various nanoscale elements with unique characteristics provides an alternative cost-effective methodology to complementary metal-oxide-semiconductors, laying the foundation for the realization of high performance logic circuits.

  10. Asteroid models from photometry and complementary data sources

    Energy Technology Data Exchange (ETDEWEB)

    Kaasalainen, Mikko [Department of Mathematics, Tampere University of Technology (Finland)

    2016-05-10

    I discuss inversion methods for asteroid shape and spin reconstruction with photometry (lightcurves) and complementary data sources such as adaptive optics or other images, occultation timings, interferometry, and range-Doppler radar data. These are essentially different sampling modes (generalized projections) of plane-of-sky images. An important concept in this approach is the optimal weighting of the various data modes. The maximum compatibility estimate, a multi-modal generalization of the maximum likelihood estimate, can be used for this purpose. I discuss the fundamental properties of lightcurve inversion by examining the two-dimensional case that, though not usable in our three-dimensional world, is simple to analyze, and it shares essentially the same uniqueness and stability properties as the 3-D case. After this, I review the main aspects of 3-D shape representations, lightcurve inversion, and the inclusion of complementary data.

  11. Asteroid models from photometry and complementary data sources

    International Nuclear Information System (INIS)

    Kaasalainen, Mikko

    2016-01-01

    I discuss inversion methods for asteroid shape and spin reconstruction with photometry (lightcurves) and complementary data sources such as adaptive optics or other images, occultation timings, interferometry, and range-Doppler radar data. These are essentially different sampling modes (generalized projections) of plane-of-sky images. An important concept in this approach is the optimal weighting of the various data modes. The maximum compatibility estimate, a multi-modal generalization of the maximum likelihood estimate, can be used for this purpose. I discuss the fundamental properties of lightcurve inversion by examining the two-dimensional case that, though not usable in our three-dimensional world, is simple to analyze, and it shares essentially the same uniqueness and stability properties as the 3-D case. After this, I review the main aspects of 3-D shape representations, lightcurve inversion, and the inclusion of complementary data.

  12. Complementary and Alternative Approaches to Pain Relief during Labor

    Directory of Open Access Journals (Sweden)

    Michel Tournaire

    2007-01-01

    Full Text Available This review evaluated the effect of complementary and alternative medicine on pain during labor with conventional scientific methods using electronic data bases through 2006 were used. Only randomized controlled trials with outcome measures for labor pain were kept for the conclusions. Many studies did not meet the scientific inclusion criteria. According to the randomized control trials, we conclude that for the decrease of labor pain and/or reduction of the need for conventional analgesic methods: (i There is an efficacy found for acupressure and sterile water blocks. (ii Most results favored some efficacy for acupuncture and hydrotherapy. (iii Studies for other complementary or alternative therapies for labor pain control have not shown their effectiveness.

  13. Complementary Cohort Strategy for Multimodal Face Pair Matching

    DEFF Research Database (Denmark)

    Sun, Yunlian; Nasrollahi, Kamal; Sun, Zhenan

    2016-01-01

    Face pair matching is the task of determining whether two face images represent the same person. Due to the limited expressive information embedded in the two face images as well as various sources of facial variations, it becomes a quite difficult problem. Towards the issue of few available images...... provided to represent each face, we propose to exploit an extra cohort set (identities in the cohort set are different from those being compared) by a series of cohort list comparisons. Useful cohort coefficients are then extracted from both sorted cohort identities and sorted cohort images...... for complementary information. To augment its robustness to complicated facial variations, we further employ multiple face modalities owing to their complementary value to each other for the face pair matching task. The final decision is made by fusing the extracted cohort coefficients with the direct matching...

  14. Polarization-independent transparency window induced by complementary graphene metasurfaces

    International Nuclear Information System (INIS)

    Lu, Wei Bing; Liu, Ji Long; Zhang, Jin; Wang, Jian; Liu, Zhen Guo

    2017-01-01

    A fourfold symmetric graphene-based complementary metasurface featuring a polarization-independent transparency window is proposed and numerically analysed in this paper. The unit cell of the metamaterial consists of a monolayer graphene perforated with a cross and four identical split-ring resonators deposited on a substrate. Our analysis shows that the transparency window can be interpreted as a plasmonic analogy of Autler–Townes splitting. The polarization independence is achieved due to the fourfold symmetry of graphene’s complementary structure. In addition, the frequency range of the transparency window can be dynamically tuned over a broad band by changing the chemical potential of graphene, and the width of the transparency window can also be controlled by changing the split-gap orientation. This work may lead to potential applications in many area, such as slow-light devices and optical sensing. (paper)

  15. Transcriptomics resources of human tissues and organs

    DEFF Research Database (Denmark)

    Uhlén, Mathias; Hallström, Björn M.; Lindskog, Cecilia

    2016-01-01

    a framework for defining the molecular constituents of the human body as well as for generating comprehensive lists of proteins expressed across tissues or in a tissue-restricted manner. Here, we review publicly available human transcriptome resources and discuss body-wide data from independent genome......Quantifying the differential expression of genes in various human organs, tissues, and cell types is vital to understand human physiology and disease. Recently, several large-scale transcriptomics studies have analyzed the expression of protein-coding genes across tissues. These datasets provide...

  16. Complementary roles of interventional radiology and therapeutic endoscopy in gastroenterology

    DEFF Research Database (Denmark)

    Ray, David M; Srinivasan, Indu; Tang, Shou-Jiang

    2017-01-01

    radiology have resulted in the paradigm shift in the management of these conditions. In this paper, we discuss the patient's work up, indications, and complementary roles of endoscopic and angiographic management in the settings of gastrointestinal bleeding, enteral feeding, cecostomy tube placement...... and luminal strictures. These conditions often require multidisciplinary approaches involving a team of interventional radiologists, gastroenterologists and surgeons. Further, the authors also aim to describe how the fields of interventional radiology and gastrointestinal endoscopy are overlapping...

  17. The leadership team: complementary strengths or conflicting agendas?

    Science.gov (United States)

    Miles, Stephen A; Watkins, Michael D

    2007-04-01

    Senior leadership teams whose members play complementary roles have been chronicled as far back as Homer's account of the Trojan War: Although King Agamemnon commanded the Greek army, Achilles, Odysseus, and Nestor each played a distinct role in defeating Troy. Today, complementary-leadership structures are common and, in some cases, even institutionalized. Think of a CEO concerned mainly with external issues and a COO who focuses internally. The authors describe four kinds of complementarity: task, expertise, cognitive, and role. The two top executives at the software company Adobe Systems, for example, represent the second kind. As CEO, Bruce Chizen draws on his sales and marketing knowledge, while COO Shantanu Narayen adds his engineering and product development expertise. Roberto Goizueta, formerly the CEO of Coca-Cola, and Douglas Ivester, his COO (who later became CEO), were famous examples of the fourth type: Goizueta, the diplomat, maintained good relations with external stakeholders; Ivester, the warrior, drove the company to defeat the competition. Bringing together two or more people with complementary strengths can compensate for the natural limitations of each. But with the benefits comes the risk of confusion, disagreement about priorities, and turf battles. Leadership succession also presents substantial challenges, especially when a COO or president who has worked in a complementary fashion with the CEO moves into the top role. An organization's board of directors and CEO can manage the risks by fostering a shared vision, common incentives, communication, and trust. They can also ensure smooth succession processes in various ways, such as brokering a gradual transfer of responsibilities or allowing the CEO and the COO to share duties as long as they maintain the logic of complementarity.

  18. Complementary and alternative exercise for fibromyalgia: a meta-analysis

    OpenAIRE

    Mist, Scott; Firestone,Kari; Jones,Kim Dupree

    2013-01-01

    Scott David Mist, Kari Firestone, Kim Dupree Jones Fibromyalgia Research and Treatment Group, School of Nursing, Oregon Health and Science University, Portland, OR, USA Abstract: Complementary and alternative medicine includes a number of exercise modalities, such as tai chi, qigong, yoga, and a variety of lesser-known movement therapies. A meta-analysis of the current literature was conducted estimating the effect size of the different modalities, study quality and bias, and adverse events....

  19. Results with Complementary Food Using Local Food Ingredients.

    Science.gov (United States)

    Ahmed, Tahmeed; Islam, Munirul; Choudhury, Nuzhat; Hossain, Iqbal; Huq, Sayeeda; Mahfuz, Mustafa; Sarker, Shafiqul Alam

    2017-01-01

    Appropriate complementary food is a must for optimum growth of infants and children. The food should be diverse and be given in sufficient quantities 2-4 times a day depending upon age. Poverty, food insecurity, and lack of awareness regarding the choice of nutritious food ingredients are deterrents to optimum complementary feeding. In Bangladesh, 77% of children do not receive appropriate complementary food and, hence, the high prevalence of childhood malnutrition. We developed ready-to-use complementary foods (RUCFs) using locally available food ingredients, rice/lentil and chickpea, which conform to standard specifications. These foods were found to be acceptable by children and their mothers compared to the Pushti packet, the cereal-based supplement used in the erstwhile National Nutrition Program of Bangladesh. In a cluster-randomized community-based trial in rural Bangladesh among more than 5,000 children, the efficacy of rice/lentil- and chickpea-based RUCFs was compared with another commonly used supplementary food called wheat-soy blend++ (WSB++) and a commercial product called Plumpy'doz. Deceleration in length for age was significantly lower (by 0.02-0.04/month) in the rice/lentil, Plumpy'doz, and chickpea groups compared to the control group at 18 months of age. Weight-for-length z-score decline was lower only in Plumpy'doz and chickpea groups. WSB++ was not different from the control group. In children who received chickpea RUCF or Plumpy'doz, the prevalence of stunting was 5-6% lower at 18 months. These foods can be used to prevent or treat malnutrition among children, particularly those from food-insecure households. © 2017 Nestec Ltd., Vevey/S. Karger AG, Basel.

  20. Complementary safety assessments - Report by the French Nuclear Safety Authority

    International Nuclear Information System (INIS)

    2011-12-01

    As an immediate consequence of the Fukushima accident, the French Authority of Nuclear Safety (ASN) launched a campaign of on-site inspections and asked operators (mainly EDF, AREVA and CEA) to make complementary assessments of the safety of the nuclear facilities they manage. The approach defined by ASN for the complementary safety assessments (CSA) is to study the behaviour of nuclear facilities in severe accidents situations caused by an off-site natural hazard according to accident scenarios exceeding the current baseline safety requirements. This approach can be broken into 2 phases: first conformity to current design and secondly an approach to the beyond design-basis scenarios built around the principle of defence in depth. 38 inspections were performed on issues linked to the causes of the Fukushima crisis. It appears that some sites have to reinforce the robustness of the heat sink. The CSA confirmed that the processes put into place at EDF to detect non-conformities were satisfactory. The complementary safety assessments demonstrated that the current seismic margins on the EDF nuclear reactors are satisfactory. With regard to flooding, the complementary safety assessments show that the complete reassessment carried out following the flooding of the Le Blayais nuclear power plant in 1999 offers the installations a high level of protection against the risk of flooding. Concerning the loss of electrical power supplies and the loss of cooling systems, the analysis of EDF's CSA reports showed that certain heat sink and electrical power supply loss scenarios can, if nothing is done, lead to core melt in just a few hours in the most unfavourable circumstances. As for nuclear facilities that are not power or experimental reactors, some difficulties have appeared to implement the CSA approach that was initially devised for reactors. Generally speaking, ASN considers that the safety of nuclear facilities must be made more robust to improbable risks which are not

  1. Synergy optimization and operation management on syndicate complementary knowledge cooperation

    Science.gov (United States)

    Tu, Kai-Jan

    2014-10-01

    The number of multi enterprises knowledge cooperation has grown steadily, as a result of global innovation competitions. I have conducted research based on optimization and operation studies in this article, and gained the conclusion that synergy management is effective means to break through various management barriers and solve cooperation's chaotic systems. Enterprises must communicate system vision and access complementary knowledge. These are crucial considerations for enterprises to exert their optimization and operation knowledge cooperation synergy to meet global marketing challenges.

  2. Zeroes of functions of Fresnel complementary integral type

    Directory of Open Access Journals (Sweden)

    Mario Alberto Villalobos Arias

    2017-02-01

    Full Text Available Theoretical upper and lower bounds are established for zeroes of a parametric family of functions which are defined by integrals of the same type as  the Fresnel complementary integral. Asymptotic properties for these bounds are obtained as well as monotony properties of the localization  intervals.  Given the value of the parameter an analytical-numerical procedure is deduced to enclose all  zeros of a given function with an a priori error.

  3. Complementary feeding: a Global Network cluster randomized controlled trial

    Directory of Open Access Journals (Sweden)

    Pasha Omrana

    2011-01-01

    Full Text Available Abstract Background Inadequate and inappropriate complementary feeding are major factors contributing to excess morbidity and mortality in young children in low resource settings. Animal source foods in particular are cited as essential to achieve micronutrient requirements. The efficacy of the recommendation for regular meat consumption, however, has not been systematically evaluated. Methods/Design A cluster randomized efficacy trial was designed to test the hypothesis that 12 months of daily intake of beef added as a complementary food would result in greater linear growth velocity than a micronutrient fortified equi-caloric rice-soy cereal supplement. The study is being conducted in 4 sites of the Global Network for Women's and Children's Health Research located in Guatemala, Pakistan, Democratic Republic of the Congo (DRC and Zambia in communities with toddler stunting rates of at least 20%. Five clusters per country were randomized to each of the food arms, with 30 infants in each cluster. The daily meat or cereal supplement was delivered to the home by community coordinators, starting when the infants were 6 months of age and continuing through 18 months. All participating mothers received nutrition education messages to enhance complementary feeding practices delivered by study coordinators and through posters at the local health center. Outcome measures, obtained at 6, 9, 12, and 18 months by a separate assessment team, included anthropometry; dietary variety and diversity scores; biomarkers of iron, zinc and Vitamin B12 status (18 months; neurocognitive development (12 and 18 months; and incidence of infectious morbidity throughout the trial. The trial was supervised by a trial steering committee, and an independent data monitoring committee provided oversight for the safety and conduct of the trial. Discussion Findings from this trial will test the efficacy of daily intake of meat commencing at age 6 months and, if beneficial, will

  4. Paediatric Pain Management: Using Complementary and Alternative Medicine

    OpenAIRE

    Evans, Subhadra; Tsao, Jennie C.I; Zeltzer, Lonnie K.

    2008-01-01

    Children undergo acute painful procedures and many also experience chronic pain.Due to their developing systems, infants and children may be at greater risk than adults for protracted pain sensitivity.There is a need to manage acute and chronic paediatric pain to reduce children's suffering and to prevent future pain problems.Consistent with a biopsychosocial perspective, complementary and alternative medicine (CAM) should be considered in management of acute and chronic paediatric pain.Altho...

  5. Complementary filter implementation in the dynamic language Lua

    Science.gov (United States)

    Sadowski, Damian; Sawicki, Aleksander; Lukšys, Donatas; Slanina, Zdenek

    2017-08-01

    The article presents the complementary filter implementation, that is used for the estimation of the pitch angle, in Lua script language. Inertial sensors as accelerometer and gyroscope were used in the study. Methods of angles estimation using acceleration and angular velocity sensors were presented in the theoretical part of the article. The operating principle of complementary filter has been presented. The prototype of Butterworth's analogue filter and its digital equivalent have been designed. Practical implementation of the issue was performed with the use of PC and DISCOVERY evaluation board equipped with STM32F01 processor, L3GD20 gyroscope and LS303DLHC accelerometer. Measurement data was transmitted by UART serial interface, then processed with the use of Lua software and luaRS232 programming library. Practical implementation was divided into two stages. In the first part, measurement data has been recorded and then processed with help of a complementary filter. In the second step, coroutines mechanism was used to filter data in real time.

  6. Contextualising complementary feeding in a broader framework for stunting prevention

    DEFF Research Database (Denmark)

    Stewart, Christine P; Iannotti, Lora; Dewey, Kathryn G

    2013-01-01

    An estimated 165 million children are stunted due to the combined effects of poor nutrition, repeated infection and inadequate psychosocial stimulation. The complementary feeding period, generally corresponding to age 6-24 months, represents an important period of sensitivity to stunting with lif......An estimated 165 million children are stunted due to the combined effects of poor nutrition, repeated infection and inadequate psychosocial stimulation. The complementary feeding period, generally corresponding to age 6-24 months, represents an important period of sensitivity to stunting...... the role of complementary feeding within the layers of contextual and causal factors that lead to stunted growth and development and the resulting short- and long-term consequences. Contextual factors are organized into the following groups: political economy; health and health care systems; education....... Effectiveness studies with a strong process evaluation component are needed to identify transdisciplinary solutions. Programme and policy interventions aimed at preventing stunting should be informed by careful assessment of these factors at all levels....

  7. [Breastfeeding, complementary feeding and risk of childhood obesity].

    Science.gov (United States)

    Sandoval Jurado, Luis; Jiménez Báez, María Valeria; Olivares Juárez, Sibli; de la Cruz Olvera, Tomas

    2016-11-01

    To evaluate the pattern of breastfeeding and weaning as a risk of obesity in pre-school children from a Primary Care Unit. Cross-sectional analytical study LOCATION: Cancun, Quintana Roo (Mexico). Children from 2-4 years of age from a Primary Care Unit. Duration of total and exclusive breastfeeding, age and food utilized for complementary feeding reported by the mother or career of the child and nutritional status assessment evaluated by body mass index (BMI) ≥ 95 percentile. Determination of prevalence ratio (PR), odds ratio (OR), chi squared (x2), and binary logistic regression. The study included 116 children (55.2% girls) with a mean age of 3.2 years, with obesity present in 62.1%, Exclusive breastfeeding in 72.4% with mean duration of 2.3 months, and age at introducing solids foods was 5.0 months. There was a difference for breastfeeding and complementary feeding by gender sex (P<.05). A PR=3.9 (95% CI: 1.49-6.34) was calculated for exclusive breastfeeding and risk of obesity. The model showed no association between these variables and obesity in children CONCLUSIONS: Exclusive breastfeeding of less than three months is associated with almost 4 more times in obese children. There was a difference in age of complementary feeding, duration of breastfeeding, and formula milk consumption time for obese and non-obese children. Copyright © 2015 Elsevier España, S.L.U. All rights reserved.

  8. Complementary/alternative medicine use among chronic pain clinic patients.

    Science.gov (United States)

    Konvicka, James J; Meyer, Tricia A; McDavid, Andrew J; Roberson, Charles R

    2008-02-01

    Complementary and alternative therapies have enjoyed increasingly widespread use in recent years. Because of this trend, we were eager to obtain a better grasp on the actual number of people in our hospital's pain clinic who have used these modalities. In an effort to explore the use of complementary/alternative medicine (CAM) by patients seen in an anesthesiology chronic pain clinic, we conducted a study using a questionnaire. This questionnaire contained two sections, one covering complementary/alternative modalities and the other dealing with herbals or nutraceuticals. More than 400 patients were surveyed, 41% of whom were male and 59% of whom were female. Comparing alternative therapies by gender revealed no statistical difference in males versus females. The most commonly chosen modalities overall were nutraceuticals, massage therapy, and acupuncture. In terms of age, we found that the patients surveyed who were older than 60 years of age preferred nutraceuticals, and that the younger age group preferred more interactive relaxation techniques, such as meditation and massage.

  9. Transcriptome analysis of adiposity in domestic ducks by transcriptomic comparison with their wild counterparts.

    Science.gov (United States)

    Chen, L; Luo, J; Li, J X; Li, J J; Wang, D Q; Tian, Y; Lu, L Z

    2015-06-01

    Excessive adiposity is a major problem in the duck industry, but its molecular mechanisms remain unknown. Genetic comparisons between domestic and wild animals have contributed to the exploration of genetic mechanisms responsible for many phenotypic traits. Significant differences in body fat mass have been detected between domestic and wild ducks. In this study, we used the Peking duck and Anas platyrhynchos as the domestic breed and wild counterpart respectively and performed a transcriptomic comparison of abdominal fat between the two breeds to comprehensively analyze the transcriptome basis of adiposity in ducks. We obtained approximately 350 million clean reads; assembled 61 250 transcripts, including 23 699 novel ones; and identified alternative 5' splice sites, alternative 3' splice sites, skipped exons and retained intron as the main alternative splicing events. A differential expression analysis between the two breeds showed that 753 genes exhibited differential expression. In Peking ducks, some lipid metabolism-related genes (IGF2, FABP5, BMP7, etc.) and oncogenes (RRM2, AURKA, CYR61, etc.) were upregulated, whereas genes related to tumor suppression and immunity (TNFRSF19, TNFAIP6, IGSF21, NCF1, etc.) were downregulated, suggesting adiposity might closely associate with tumorigenesis in ducks. Furthermore, 280 576 single-nucleotide variations were found differentiated between the two breeds, including 8641 non-synonymous ones, and some of the non-synonymous ones were found enriched in genes involved in lipid-associated and immune-associated pathways, suggesting abdominal fat of the duck undertakes both a metabolic function and immune-related function. These datasets enlarge our genetic information of ducks and provide valuable resources for analyzing mechanisms underlying adiposity in ducks. © 2015 Stichting International Foundation for Animal Genetics.

  10. Systematic reviews of complementary therapies - an annotated bibliography. Part 3: homeopathy

    NARCIS (Netherlands)

    Linde, K.; Hondras, M.; Vickers, A.; ter Riet, G.; Melchart, D.

    2001-01-01

    BACKGROUND: Complementary therapies are widespread but controversial. We aim to provide a comprehensive collection and a summary of systematic reviews of clinical trials in three major complementary therapies (acupuncture, herbal medicine, homeopathy). This article is dealing with homeopathy.

  11. Systematic reviews of complementary therapies - an annotated bibliography. Part 2: herbal medicine

    NARCIS (Netherlands)

    Linde, K.; ter Riet, G.; Hondras, M.; Vickers, A.; Saller, R.; Melchart, D.

    2001-01-01

    BACKGROUND: Complementary therapies are widespread but controversial. We aim to provide a comprehensive collection and a summary of systematic reviews of clinical trials in three major complementary therapies (acupuncture, herbal medicine, homeopathy). This article is dealing with herbal medicine.

  12. 76 FR 30735 - National Center for Complementary & Alternative Medicine; Notice of Closed Meeting

    Science.gov (United States)

    2011-05-26

    ... Complementary & Alternative Medicine; Notice of Closed Meeting Pursuant to section 10(d) of the Federal Advisory..., Scientific Review Officer, National Center for Complementary and Alternative Medicine, National Institutes of... Alternative Medicine [[Page 30736

  13. A novel pseudo-complementary PNA G-C base pair

    DEFF Research Database (Denmark)

    Olsen, Anne G.; Dahl, Otto; Petersen, Asger Bjørn

    2011-01-01

    Pseudo-complementary oligonucleotide analogues and mimics provide novel opportunities for targeting duplex structures in RNA and DNA. Previously, a pseudo-complementary A-T base pair has been introduced. Towards sequence unrestricted targeting, a pseudo-complementary G-C base pair consisting...

  14. 77 FR 69869 - National Center for Complementary and Alternative Medicine; Notice of Closed Meeting

    Science.gov (United States)

    2012-11-21

    ... Complementary and Alternative Medicine; Notice of Closed Meeting Pursuant to section 10(d) of the Federal... Alternative Medicine Special Emphasis Panel, PAR 12-151: Centers of Excellence for Research on Complementary... Review, National Center for Complementary, & Alternative Medicine, NIH, 6707 Democracy Blvd., Suite 401...

  15. 77 FR 52750 - National Center for Complementary & Alternative Medicine; Notice of Meeting

    Science.gov (United States)

    2012-08-30

    ... Complementary & Alternative Medicine; Notice of Meeting Pursuant to section 10(d) of the Federal Advisory... Council for Complementary and Alternative Medicine. The meeting will be open to the public as indicated... privacy. Name of Committee: National Advisory Council for Complementary and Alternative Medicine. Date...

  16. 77 FR 28396 - National Center for Complementary & Alternative Medicine Notice of Closed Meeting

    Science.gov (United States)

    2012-05-14

    ... Complementary & Alternative Medicine Notice of Closed Meeting Pursuant to section 10(d) of the Federal Advisory... Alternative Medicine Special Emphasis Pane,l Clinical Research of Complementary Medical Care. Date: June 5.... 93.213, Research and Training in Complementary and Alternative Medicine, National Institutes of...

  17. 75 FR 76019 - National Center for Complementary & Alternative Medicine; Notice of Meeting

    Science.gov (United States)

    2010-12-07

    ... Complementary & Alternative Medicine; Notice of Meeting Pursuant to section 10(d) of the Federal Advisory... Complementary and Alternative Medicine (NACCAM) meeting. The meeting will be open to the public as indicated... for Complementary and Alternative Medicine. Date: February 4, 2011. Closed: February 4, 2011, 8:30 a.m...

  18. 78 FR 19498 - National Center for Complementary and Alternative Medicine; Notice of Meeting

    Science.gov (United States)

    2013-04-01

    ... Complementary and Alternative Medicine; Notice of Meeting Pursuant to section 10(d) of the Federal Advisory... Council for Complementary and Alternative Medicine. The meeting will be open to the public as indicated... privacy. Name of Committee: National Advisory Council for Complementary and Alternative Medicine. Date...

  19. 78 FR 76635 - National Center for Complementary and Alternative Medicine; Notice of Meeting

    Science.gov (United States)

    2013-12-18

    ... Complementary and Alternative Medicine; Notice of Meeting Pursuant to section 10(d) of the Federal Advisory... Council for Complementary and Alternative Medicine. The meeting will be open to the public as indicated... privacy. Name of Committee: National Advisory Council for Complementary and Alternative Medicine; NCCAM...

  20. 76 FR 79202 - National Center for Complementary & Alternative Medicine; Notice of Meeting

    Science.gov (United States)

    2011-12-21

    ... Complementary & Alternative Medicine; Notice of Meeting Pursuant to section 10(d) of the Federal Advisory... Council for Complementary and Alternative Medicine. The meeting will be open to the public as indicated... privacy. Name of Committee: National Advisory Council for Complementary and Alternative Medicine. Date...

  1. 75 FR 35075 - National Center for Complementary & Alternative Medicine; Notice of Closed Meeting

    Science.gov (United States)

    2010-06-21

    ... Complementary & Alternative Medicine; Notice of Closed Meeting Pursuant to section 10(d) of the Federal Advisory..., Office of Scientific Review, National Center for Complementary, & Alternative Medicine, NIH, 6707... Domestic Assistance Program Nos. 93.213, Research and Training in Complementary and Alternative Medicine...

  2. 75 FR 43994 - National Center for Complementary and Alternative Medicine; Notice of Meeting

    Science.gov (United States)

    2010-07-27

    ... Complementary and Alternative Medicine; Notice of Meeting Pursuant to section 10(d) of the Federal Advisory... Complementary and Alternative Medicine (NACCAM) meeting. The meeting will be open to the public as indicated... privacy. Name of Committee: National Advisory Council for Complementary and Alternative Medicine. Date...

  3. 76 FR 35227 - National Center for Complementary & Alternative Medicine; Notice of Closed Meeting

    Science.gov (United States)

    2011-06-16

    ... Complementary & Alternative Medicine; Notice of Closed Meeting Pursuant to section 10(d) of the Federal Advisory... Scientific Review, National Center for Complementary, and Alternative Medicine, NIH, 6707 Democracy Blvd... Assistance Program Nos. 93.213, Research and Training in Complementary and Alternative Medicine, National...

  4. 78 FR 47328 - National Center for Complementary & Alternative Medicine; Notice of Closed Meeting

    Science.gov (United States)

    2013-08-05

    ... Complementary & Alternative Medicine; Notice of Closed Meeting Pursuant to section 10(d) of the Federal Advisory..., Ph.D., Scientific Review Officer, National Center For Complementary and Alternative Medicine... Training in Complementary and Alternative Medicine, National Institutes of Health, HHS) Dated: July 30...

  5. 77 FR 43099 - National Center For Complementary & Alternative Medicine; Notice of Closed Meeting

    Science.gov (United States)

    2012-07-23

    ... Complementary & Alternative Medicine; Notice of Closed Meeting Pursuant to section 10(d) of the Federal Advisory... Council for Complementary and Alternative Medicine. The meeting will be closed to the public in accordance... of Committee: National Advisory Council for Complementary and Alternative Medicine. Date: August 27...

  6. 77 FR 25185 - National Center for Complementary and Alternative Medicine; Notice of Meeting

    Science.gov (United States)

    2012-04-27

    ... Complementary and Alternative Medicine; Notice of Meeting Pursuant to section 10(d) of the Federal Advisory... Council for Complementary and Alternative Medicine. The meeting will be open to the public as indicated... privacy. Name of Committee: National Advisory Council for Complementary and Alternative Medicine. Date...

  7. 78 FR 66755 - National Center for Complementary & Alternative Medicine; Notice of Closed Meeting

    Science.gov (United States)

    2013-11-06

    ... Complementary & Alternative Medicine; Notice of Closed Meeting Pursuant to section 10(d) of the Federal Advisory... Scientific Review, National Center for Complementary, & Alternative Medicine, NIH, 6707 Democracy Blvd... Assistance Program Nos. 93.213, Research and Training in Complementary and Alternative Medicine, National...

  8. 76 FR 19379 - National Center for Complementary & Alternative Medicine; Notice of Meeting

    Science.gov (United States)

    2011-04-07

    ... Complementary & Alternative Medicine; Notice of Meeting Pursuant to section 10(d) of the Federal Advisory... Complementary and Alternative Medicine (NACCAM) meeting. The meeting will be open to the public as indicated... for Complementary and Alternative Medicine. Date: June 3, 2011. Closed: June 3, 2011, 8:30 a.m. to 10...

  9. 78 FR 42528 - National Center for Complementary & Alternative Medicine; Notice of Closed Meeting

    Science.gov (United States)

    2013-07-16

    ... Complementary & Alternative Medicine; Notice of Closed Meeting Pursuant to section 10(d) of the Federal Advisory... Center for Complementary & Alternative Medicine, NIH, 6707 Democracy Blvd., Suite 401, Bethesda, MD 20892..., Research and Training in Complementary and Alternative Medicine, National Institutes of Health, HHS) Dated...

  10. 76 FR 55073 - National Center for Complementary & Alternative Medicine; Notice of Closed Meeting

    Science.gov (United States)

    2011-09-06

    ... Complementary & Alternative Medicine; Notice of Closed Meeting Pursuant to section 10(d) of the Federal Advisory... Complementary and Alternative Medicine (NACCAM) meeting. The meeting will be open to the public as indicated... Advisory Council for Complementary and Alternative Medicine. Date: October 14, 2011. Closed: October 14...

  11. 78 FR 10184 - National Center For Complementary & Alternative Medicine; Notice of Closed Meetings

    Science.gov (United States)

    2013-02-13

    ... Complementary & Alternative Medicine; Notice of Closed Meetings Pursuant to section 10(d) of the Federal... Alternative Medicine Special Emphasis Panel; Clinical Studies of Complementary and Alternative Medicine. Date... Person: Hungyi Shau, Ph.D., Scientific Review Officer, National Center For Complementary, and Alternative...

  12. 75 FR 19979 - National Center for Complementary and Alternative Medicine Announcement of Workshop on the...

    Science.gov (United States)

    2010-04-16

    ... Complementary and Alternative Medicine Announcement of Workshop on the Deconstruction of Back Pain ACTION: Notice. SUMMARY: The National Center for Complementary and Alternative Medicine (NCCAM) invites the... Alternative Medicine (NCCAM) was established in 1999 with the mission of exploring complementary and...

  13. 76 FR 17140 - National Center for Complementary & Alternative Medicine; Notice of Closed Meeting

    Science.gov (United States)

    2011-03-28

    ... Complementary & Alternative Medicine; Notice of Closed Meeting Pursuant to section 10(d) of the Federal Advisory... Complementary and Alternative Medicine, National Institutes of Health, 6707 Democracy Boulevard, Suite 401... Nos. 93.213, Research and Training in Complementary and Alternative Medicine, National Institutes of...

  14. 75 FR 63498 - National Center for Complementary and Alternative Medicine; Notice of Closed Meeting

    Science.gov (United States)

    2010-10-15

    ... Complementary and Alternative Medicine; Notice of Closed Meeting Pursuant to section 10(d) of the Federal...: Hungyi Shau, Scientific Review Officer, National Center for Complementary and Alternative Medicine... Training in Complementary and Alternative Medicine, National Institutes of Health, HHS) Dated: October 5...

  15. 75 FR 30039 - National Center for Complementary and Alternative Medicine; Notice of Closed Meetings

    Science.gov (United States)

    2010-05-28

    ... Complementary and Alternative Medicine; Notice of Closed Meetings Pursuant to section 10(d) of the Federal... Complementary and Alternative Medicine Special Emphasis Panel; Education Panel. Date: June 24-25, 2010. Time: 5... of Committee: National Center for Complementary and Alternative Medicine Special Emphasis Panel; RFA...

  16. 78 FR 21381 - National Center for Complementary & Alternative Medicine; Notice of Closed Meeting

    Science.gov (United States)

    2013-04-10

    ... Complementary & Alternative Medicine; Notice of Closed Meeting Pursuant to section 10(d) of the Federal Advisory... Complementary and Alternative Medicine Special Emphasis Education Panel. Date: June 21, 2013. Time: 8:00 a.m. to... Complementary and Alternative Medicine, National Institutes of Health, HHS) Dated: April 4, 2013. Michelle Trout...

  17. 77 FR 58402 - National Center for Complementary & Alternative Medicine; Notice of Closed Meeting

    Science.gov (United States)

    2012-09-20

    ... Complementary & Alternative Medicine; Notice of Closed Meeting Pursuant to section 10(d) of the Federal Advisory... Alternative Medicine Special Emphasis Panel; Clinical Research of Complementary Medical Care. Date: October 22...: Hungyi Shau, Ph.D., Scientific Review Officer, National Center For Complementary and Alternative Medicine...

  18. 75 FR 57970 - National Center for Complementary & Alternative Medicine; Notice of Closed Meeting

    Science.gov (United States)

    2010-09-23

    ... Complementary & Alternative Medicine; Notice of Closed Meeting Pursuant to section 10(d) of the Federal Advisory... Complementary and Alternative Medicine Special Emphasis Panel, Centers of Excellence for Research on CAM (CERC... Complementary, & Alternative Medicine, NIH, 6707 Democracy Blvd., Suite 401, Bethesda, MD 20892, 301-594-3456...

  19. 77 FR 24971 - National Center for Complementary & Alternative Medicine; Notice of Closed Meeting

    Science.gov (United States)

    2012-04-26

    ... Complementary & Alternative Medicine; Notice of Closed Meeting Pursuant to section 10(d) of the Federal Advisory..., [email protected] . Name of Committee: National Center for Complementary and Alternative Medicine..., Office of Scientific Review, National Center for Complementary & Alternative Medicine, NIH, 6707...

  20. 75 FR 12769 - National Center for Complementary and Alternative Medicine Announcement of Workshop on Control...

    Science.gov (United States)

    2010-03-17

    ... Complementary and Alternative Medicine Announcement of Workshop on Control/Comparison Groups for Trials of Non... Complementary and Alternative Medicine (NCCAM) was established in 1998 with the mission of exploring... Center for Complementary and Alternative Medicine, National Institutes of Health. [FR Doc. 2010-5767...

  1. 77 FR 73036 - National Center for Complementary & Alternative Medicine; Notice of Meeting

    Science.gov (United States)

    2012-12-07

    ... Complementary & Alternative Medicine; Notice of Meeting Pursuant to section 10(d) of the Federal Advisory... Council for Complementary and Alternative Medicine. The meeting will be open to the public as indicated... privacy. Name of Committee: National Advisory Council for Complementary and Alternative Medicine. Date...

  2. 75 FR 13137 - National Center For Complementary and Alternative Medicine; Notice of Closed Meeting

    Science.gov (United States)

    2010-03-18

    ... Complementary and Alternative Medicine; Notice of Closed Meeting Pursuant to section 10(d) of the Federal... Complementary and Alternative Medicine, NIH, 6707 Democracy Blvd., Suite 401, Bethesda, MD 20892, (301) 451-6570... Training in Complementary and Alternative Medicine, National Institutes of Health, HHS) Dated: March 10...

  3. 76 FR 59707 - National Center for Complementary & Alternative Medicine; Notice of Closed Meetings

    Science.gov (United States)

    2011-09-27

    ... Complementary & Alternative Medicine; Notice of Closed Meetings Pursuant to section 10(d) of the Federal... for Complementary and Alternative Medicine Special Emphasis Panel, Training and Education. Date... Complementary and Alternative Medicine Special Emphasis Panel, Clinical Studies of CAM Therapies. Date: November...

  4. Comparative genomics reveals conservative evolution of the xylem transcriptome in vascular plants.

    Science.gov (United States)

    Li, Xinguo; Wu, Harry X; Southerton, Simon G

    2010-06-21

    Wood is a valuable natural resource and a major carbon sink. Wood formation is an important developmental process in vascular plants which played a crucial role in plant evolution. Although genes involved in xylem formation have been investigated, the molecular mechanisms of xylem evolution are not well understood. We use comparative genomics to examine evolution of the xylem transcriptome to gain insights into xylem evolution. The xylem transcriptome is highly conserved in conifers, but considerably divergent in angiosperms. The functional domains of genes in the xylem transcriptome are moderately to highly conserved in vascular plants, suggesting the existence of a common ancestral xylem transcriptome. Compared to the total transcriptome derived from a range of tissues, the xylem transcriptome is relatively conserved in vascular plants. Of the xylem transcriptome, cell wall genes, ancestral xylem genes, known proteins and transcription factors are relatively more conserved in vascular plants. A total of 527 putative xylem orthologs were identified, which are unevenly distributed across the Arabidopsis chromosomes with eight hot spots observed. Phylogenetic analysis revealed that evolution of the xylem transcriptome has paralleled plant evolution. We also identified 274 conifer-specific xylem unigenes, all of which are of unknown function. These xylem orthologs and conifer-specific unigenes are likely to have played a crucial role in xylem evolution. Conifers have highly conserved xylem transcriptomes, while angiosperm xylem transcriptomes are relatively diversified. Vascular plants share a common ancestral xylem transcriptome. The xylem transcriptomes of vascular plants are more conserved than the total transcriptomes. Evolution of the xylem transcriptome has largely followed the trend of plant evolution.

  5. 20180311 - High Throughput Transcriptomics: From screening to pathways (SOT 2018)

    Science.gov (United States)

    The EPA ToxCast effort has screened thousands of chemicals across hundreds of high-throughput in vitro screening assays. The project is now leveraging high-throughput transcriptomic (HTTr) technologies to substantially expand its coverage of biological pathways. The first HTTr sc...

  6. Transcriptome Profiling in Human Diseases: New Advances and Perspectives

    Directory of Open Access Journals (Sweden)

    Amelia Casamassimi

    2017-07-01

    Full Text Available In the last decades, transcriptome profiling has been one of the most utilized approaches to investigate human diseases at the molecular level. Through expression studies, many molecular biomarkers and therapeutic targets have been found for several human pathologies. This number is continuously increasing thanks to total RNA sequencing. Indeed, this new technology has completely revolutionized transcriptome analysis allowing the quantification of gene expression levels and allele-specific expression in a single experiment, as well as to identify novel genes, splice isoforms, fusion transcripts, and to investigate the world of non-coding RNA at an unprecedented level. RNA sequencing has also been employed in important projects, like ENCODE (Encyclopedia of the regulatory elements and TCGA (The Cancer Genome Atlas, to provide a snapshot of the transcriptome of dozens of cell lines and thousands of primary tumor specimens. Moreover, these studies have also paved the way to the development of data integration approaches in order to facilitate management and analysis of data and to identify novel disease markers and molecular targets to use in the clinics. In this scenario, several ongoing clinical trials utilize transcriptome profiling through RNA sequencing strategies as an important instrument in the diagnosis of numerous human pathologies.

  7. A pathology atlas of the human cancer transcriptome

    DEFF Research Database (Denmark)

    Uhlén, Mathias; Zhang, Xi-Cheng; Lee, Sunjae

    2017-01-01

    Cancer is one of the leading causes of death, and there is great interest in understanding the underlying molecular mechanisms involved in the pathogenesis and progression of individual tumors. We used systems-level approaches to analyze the genome-wide transcriptome of the protein-coding genes o...

  8. Transcriptome and genome size analysis of the venus flytrap

    DEFF Research Database (Denmark)

    Jensen, Michael Krogh; Vogt, Josef Korbinian; Bressendorff, Simon

    2015-01-01

    . muscipula flowers and traps. Using the Oases transcriptome assembler 79,165,657 quality trimmed reads were assembled into 80,806 cDNA contigs, with an average length of 679 bp and an N50 length of 1,051 bp. A total of 17,047 unique proteins were identified, and assigned to Gene Ontology (GO) and classified...

  9. Minor class splicing shapes the zebrafish transcriptome during development

    DEFF Research Database (Denmark)

    Markmiller, Sebastian; Cloonan, Nicole; Lardelli, Rea M

    2014-01-01

    known as Taybi-Linder syndrome or microcephalic osteodysplastic primordial dwarfism 1, and a hereditary intestinal polyposis condition, Peutz-Jeghers syndrome. Although a key mechanism for regulating gene expression, the impact of impaired U12-type splicing on the transcriptome is unknown. Here, we...

  10. Transcriptomes of the desiccation- tolerant resurrection plant Craterostigma plantagineum

    DEFF Research Database (Denmark)

    Rodriguez, M. C.; Edsgard, Stefan Daniel; Hussain, S. S.

    2010-01-01

    the transcriptomes of C. plantagineum leaves at four stages of dehydration and rehydration. This reveals that genes involved in several pathways, such as those required for vitamin K and thiamin biosynthesis, are tightly regulated at the level of gene expression. Our analysis also provides a comprehensive picture...

  11. Single cell transcriptome profiling of developing chick retinal cells.

    Science.gov (United States)

    Laboissonniere, Lauren A; Martin, Gregory M; Goetz, Jillian J; Bi, Ran; Pope, Brock; Weinand, Kallie; Ellson, Laura; Fru, Diane; Lee, Miranda; Wester, Andrea K; Liu, Peng; Trimarchi, Jeffrey M

    2017-08-15

    The vertebrate retina is a specialized photosensitive tissue comprised of six neuronal and one glial cell types, each of which develops in prescribed proportions at overlapping timepoints from a common progenitor pool. While each of these cells has a specific function contributing to proper vision in the mature animal, their differential representation in the retina as well as the presence of distinctive cellular subtypes makes identifying the transcriptomic signatures that lead to each retinal cell's fate determination and development challenging. We have analyzed transcriptomes from individual cells isolated from the chick retina throughout retinogenesis. While we focused our efforts on the retinal ganglion cells, our transcriptomes of developing chick cells also contained representation from multiple retinal cell types, including photoreceptors and interneurons at different stages of development. Most interesting was the identification of transcriptomes from individual mixed lineage progenitor cells in the chick as these cells offer a window into the cell fate decision-making process. Taken together, these data sets will enable us to uncover the most critical genes acting in the steps of cell fate determination and early differentiation of various retinal cell types. © 2017 Wiley Periodicals, Inc.

  12. Illumina-based de novo transcriptome sequencing and analysis

    Indian Academy of Sciences (India)

    In the present study, we used Illumina HiSeq technology to perform de novo assembly of heart and musk gland transcriptomes from the Chinese forest musk deer. A total of 239,383 transcripts and 176,450 unigenes were obtained, of which 37,329 unigenes were matched to known sequences in the NCBI nonredundant ...

  13. Transcriptome of the Antarctic brooding gastropod mollusc Margarella antarctica.

    Science.gov (United States)

    Clark, Melody S; Thorne, Michael A S

    2015-12-01

    454 RNA-Seq transcriptome data were generated from foot tissue of the Antarctic brooding gastropod mollusc Margarella antarctica. A total of 6195 contigs were assembled de novo, providing a useful resource for researchers with an interest in Antarctic marine species, phylogenetics and mollusc biology, especially shell production. Copyright © 2015 Elsevier B.V. All rights reserved.

  14. Transcriptome dynamics-based operon prediction in prokaryotes.

    Science.gov (United States)

    Fortino, Vittorio; Smolander, Olli-Pekka; Auvinen, Petri; Tagliaferri, Roberto; Greco, Dario

    2014-05-16

    Inferring operon maps is crucial to understanding the regulatory networks of prokaryotic genomes. Recently, RNA-seq based transcriptome studies revealed that in many bacterial species the operon structure vary with the change of environmental conditions. Therefore, new computational solutions that use both static and dynamic data are necessary to create condition specific operon predictions. In this work, we propose a novel classification method that integrates RNA-seq based transcriptome profiles with genomic sequence features to accurately identify the operons that are expressed under a measured condition. The classifiers are trained on a small set of confirmed operons and then used to classify the remaining gene pairs of the organism studied. Finally, by linking consecutive gene pairs classified as operons, our computational approach produces condition-dependent operon maps. We evaluated our approach on various RNA-seq expression profiles of the bacteria Haemophilus somni, Porphyromonas gingivalis, Escherichia coli and Salmonella enterica. Our results demonstrate that, using features depending on both transcriptome dynamics and genome sequence characteristics, we can identify operon pairs with high accuracy. Moreover, the combination of DNA sequence and expression data results in more accurate predictions than each one alone. We present a computational strategy for the comprehensive analysis of condition-dependent operon maps in prokaryotes. Our method can be used to generate condition specific operon maps of many bacterial organisms for which high-resolution transcriptome data is available.

  15. De novo transcriptome assembly of heavy metal tolerant Silene dioica

    Czech Academy of Sciences Publication Activity Database

    Čegan, R.; Hudzieczek, V.; Hobza, Roman

    2017-01-01

    Roč. 11, MAR (2017), s. 118-119 ISSN 2213-5960 Institutional support: RVO:61389030 Keywords : genome * Silene dioica * RNA-Seq * Transcriptome * Heavy metal tolerance * Sex chromosomes Subject RIV: EB - Genetics ; Molecular Biology OBOR OECD: Plant sciences, botany

  16. Transcriptome of barley under three different heavy metal stress reaction

    Czech Academy of Sciences Publication Activity Database

    Kintlová, Martina; Blavet, Nicolas; Cegan, R.; Hobza, Roman

    2017-01-01

    Roč. 13, SEP (2017), s. 15-17 ISSN 2213-5960 R&D Projects: GA ČR GBP501/12/G090 Institutional support: RVO:61389030 Keywords : plants * Barley * RNA-Seq * Transcriptome * Heavy metal * Copper * Zinc * Cadmium Subject RIV: EB - Genetics ; Molecular Biology OBOR OECD: Plant sciences, botany

  17. Transcriptome Profiling in Human Diseases: New Advances and Perspectives.

    Science.gov (United States)

    Casamassimi, Amelia; Federico, Antonio; Rienzo, Monica; Esposito, Sabrina; Ciccodicola, Alfredo

    2017-07-29

    In the last decades, transcriptome profiling has been one of the most utilized approaches to investigate human diseases at the molecular level. Through expression studies, many molecular biomarkers and therapeutic targets have been found for several human pathologies. This number is continuously increasing thanks to total RNA sequencing. Indeed, this new technology has completely revolutionized transcriptome analysis allowing the quantification of gene expression levels and allele-specific expression in a single experiment, as well as to identify novel genes, splice isoforms, fusion transcripts, and to investigate the world of non-coding RNA at an unprecedented level. RNA sequencing has also been employed in important projects, like ENCODE (Encyclopedia of the regulatory elements) and TCGA (The Cancer Genome Atlas), to provide a snapshot of the transcriptome of dozens of cell lines and thousands of primary tumor specimens. Moreover, these studies have also paved the way to the development of data integration approaches in order to facilitate management and analysis of data and to identify novel disease markers and molecular targets to use in the clinics. In this scenario, several ongoing clinical trials utilize transcriptome profiling through RNA sequencing strategies as an important instrument in the diagnosis of numerous human pathologies.

  18. Bacillus anthracis genome organization in light of whole transcriptome sequencing

    Energy Technology Data Exchange (ETDEWEB)

    Martin, Jeffrey; Zhu, Wenhan; Passalacqua, Karla D.; Bergman, Nicholas; Borodovsky, Mark

    2010-03-22

    Emerging knowledge of whole prokaryotic transcriptomes could validate a number of theoretical concepts introduced in the early days of genomics. What are the rules connecting gene expression levels with sequence determinants such as quantitative scores of promoters and terminators? Are translation efficiency measures, e.g. codon adaptation index and RBS score related to gene expression? We used the whole transcriptome shotgun sequencing of a bacterial pathogen Bacillus anthracis to assess correlation of gene expression level with promoter, terminator and RBS scores, codon adaptation index, as well as with a new measure of gene translational efficiency, average translation speed. We compared computational predictions of operon topologies with the transcript borders inferred from RNA-Seq reads. Transcriptome mapping may also improve existing gene annotation. Upon assessment of accuracy of current annotation of protein-coding genes in the B. anthracis genome we have shown that the transcriptome data indicate existence of more than a hundred genes missing in the annotation though predicted by an ab initio gene finder. Interestingly, we observed that many pseudogenes possess not only a sequence with detectable coding potential but also promoters that maintain transcriptional activity.

  19. Transcriptome profiling reveals regulatory mechanisms underlying Corolla Senescence in Petunia

    Science.gov (United States)

    Genetic regulatory mechanisms that govern petal natural senescence in petunia is complicated and unclear. To identify key genes and pathways that regulate the process, we initiated a transcriptome analysis in petunia petals at four developmental time points, including petal opening without anthesis ...

  20. Construction of an EST-SSR-based interspecific transcriptome ...

    Indian Academy of Sciences (India)

    Construction of an EST-SSR-based interspecific transcriptome linkage map of fibre development in cotton. CHUANXIANG LIU, DAOJUN YUAN and ZHONGXU LIN. ∗. National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan),. Huazhong Agricultural University, Wuhan ...