62 results on '"Burla B"'
Search Results
2. Population-based plasma lipidomics reveals developmental changes in metabolism and signatures of obesity risk: a mother-offspring cohort study
- Author
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Mir, SA, Chen, L, Burugupalli, S, Burla, B, Ji, S, Smith, AAT, Narasimhan, K, Ramasamy, A, Tan, KM-L, Huynh, K, Giles, C, Mei, D, Wong, G, Yap, F, Tan, KH, Collier, F, Saffery, R, Vuillermin, P, Bendt, AK, Burgner, D, Ponsonby, A-L, Lee, YS, Chong, YS, Gluckman, PD, Eriksson, JG, Meikle, PJ, Wenk, MR, Karnani, N, Mir, SA, Chen, L, Burugupalli, S, Burla, B, Ji, S, Smith, AAT, Narasimhan, K, Ramasamy, A, Tan, KM-L, Huynh, K, Giles, C, Mei, D, Wong, G, Yap, F, Tan, KH, Collier, F, Saffery, R, Vuillermin, P, Bendt, AK, Burgner, D, Ponsonby, A-L, Lee, YS, Chong, YS, Gluckman, PD, Eriksson, JG, Meikle, PJ, Wenk, MR, and Karnani, N
- Abstract
BACKGROUND: Lipids play a vital role in health and disease, but changes to their circulating levels and the link with obesity remain poorly characterized in expecting mothers and their offspring in early childhood. METHODS: LC-MS/MS-based quantitation of 480 lipid species was performed on 2491 plasma samples collected at 4 time points in the mother-offspring Asian cohort GUSTO (Growing Up in Singapore Towards healthy Outcomes). These 4 time points constituted samples collected from mothers at 26-28 weeks of gestation (n=752) and 4-5 years postpartum (n=650), and their offspring at birth (n=751) and 6 years of age (n=338). Linear regression models were used to identify the pregnancy and developmental age-specific variations in the plasma lipidomic profiles, and their association with obesity risk. An independent birth cohort (n=1935), the Barwon Infant Study (BIS), comprising mother-offspring dyads of Caucasian origin was used for validation. RESULTS: Levels of 36% of the profiled lipids were significantly higher (absolute fold change > 1.5 and Padj < 0.05) in antenatal maternal circulation as compared to the postnatal phase, with phosphatidylethanolamine levels changing the most. Compared to antenatal maternal lipids, cord blood showed lower concentrations of most lipid species (79%) except lysophospholipids and acylcarnitines. Changes in lipid concentrations from birth to 6 years of age were much higher in magnitude (log2FC=-2.10 to 6.25) than the changes observed between a 6-year-old child and an adult (postnatal mother) (log2FC=-0.68 to 1.18). Associations of cord blood lipidomic profiles with birth weight displayed distinct trends compared to the lipidomic profiles associated with child BMI at 6 years. Comparison of the results between the child and adult BMI identified similarities in association with consistent trends (R2=0.75). However, large number of lipids were associated with BMI in adults (67%) compared to the children (29%). Pre-pregnancy BMI was specif
- Published
- 2022
3. Simulation of growth and productivity of rice (Oryza sativa) under tropical monsoon climate
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Kar, Gouranga, Kumar, Ashwani, and Burla, B. Chandra Bhaskar
- Published
- 2009
4. Shared reference materials harmonize lipidomics across MS-based detection platforms and laboratories[S]
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Triebl, A, Burla, B, Selvalatchmanan, J, Oh, J, Tan, SH, Chan, MY, Mellett, NA, Meikle, PJ, Torta, F, Wenk, MR, Triebl, A, Burla, B, Selvalatchmanan, J, Oh, J, Tan, SH, Chan, MY, Mellett, NA, Meikle, PJ, Torta, F, and Wenk, MR
- Abstract
Quantitative MS of human plasma lipids is a promising technology for translation into clinical applications. Current MS-based lipidomic methods rely on either direct infusion (DI) or chromatographic lipid separation methods (including reversed phase and hydrophilic interaction LC). However, the use of lipid markers in laboratory medicine is limited by the lack of reference values, largely because of considerable differences in the concentrations measured by different laboratories worldwide. These inconsistencies can be explained by the use of different sample preparation protocols, method-specific calibration procedures, and other experimental and data-reporting parameters, even when using identical starting materials. Here, we systematically investigated the roles of some of these variables in multiple approaches to lipid analysis of plasma samples from healthy adults by considering: 1) different sample introduction methods (separation vs. DI methods); 2) different MS instruments; and 3) between-laboratory differences in comparable analytical platforms. Each of these experimental variables resulted in different quantitative results, even with the inclusion of isotope-labeled internal standards for individual lipid classes. We demonstrated that appropriate normalization to commonly available reference samples (i.e., "shared references") can largely correct for these systematic method-specific quantitative biases. Thus, to harmonize data in the field of lipidomics, in-house long-term references should be complemented by a commonly available shared reference sample, such as NIST SRM 1950, in the case of human plasma.
- Published
- 2020
5. MS-based lipidomics of human blood plasma: a community-initiated position paper to develop accepted guidelines
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Burla, B, Arita, M, Bendt, AK, Cazenave-Gassiot, A, Dennis, EA, Ekroos, K, Han, X, Ikeda, K, Liebisch, G, Lin, MK, Loh, TP, Meikle, PJ, Oresic, M, Quehenberger, O, Shevchenko, A, Torta, F, Wakelam, MJO, Wheelock, CE, Wenk, MR, Burla, B, Arita, M, Bendt, AK, Cazenave-Gassiot, A, Dennis, EA, Ekroos, K, Han, X, Ikeda, K, Liebisch, G, Lin, MK, Loh, TP, Meikle, PJ, Oresic, M, Quehenberger, O, Shevchenko, A, Torta, F, Wakelam, MJO, Wheelock, CE, and Wenk, MR
- Abstract
Human blood is a self-regenerating lipid-rich biological fluid that is routinely collected in hospital settings. The inventory of lipid molecules found in blood plasma (plasma lipidome) offers insights into individual metabolism and physiology in health and disease. Disturbances in the plasma lipidome also occur in conditions that are not directly linked to lipid metabolism; therefore, plasma lipidomics based on MS is an emerging tool in an array of clinical diagnostics and disease management. However, challenges exist in the translation of such lipidomic data to clinical applications. These relate to the reproducibility, accuracy, and precision of lipid quantitation, study design, sample handling, and data sharing. This position paper emerged from a workshop that initiated a community-led process to elaborate and define a set of generally accepted guidelines for quantitative MS-based lipidomics of blood plasma or serum, with harmonization of data acquired on different instrumentation platforms across independent laboratories as an ultimate goal. We hope that other fields may benefit from and follow such a precedent.
- Published
- 2018
6. Vacuolar Transport of Abscisic Acid Glucosyl Ester is Mediated by ATP-Binding Cassette and Proton-Antiport Mechanisms in Arabidopsis thaliana
- Author
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Burla B, Pfrunder S, Nagy R, Francisco R, Lee Y, and Martinoia E
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organic chemicals ,fungi ,food and beverages - Abstract
Abscisic acid (ABA) is a key plant hormone involved in diverse physiological and developmental processes including abiotic stress responses and the regulation of stomatal aperture and seed germination. Abscisic acid glucosyl ester (ABA GE) is a hydrolyzable ABA conjugate that accumulates in the vacuole and presumably also in the endoplasmic reticulum. Deconjugation of ABA GE by the endoplasmic reticulum and vacuolar b glucosidases allows the rapid formation of free ABA in response to abiotic stress conditions such as dehydration and salt stress. ABA GE further contributes to the maintenance of ABA homeostasis as it is the major ABA catabolite exported from the cytosol. In this work we identified that the import of ABA GE into vacuoles isolated from Arabidopsis (Arabidopsis thaliana) mesophyll cells is mediated by two distinct membrane transport mechanisms: proton gradient driven and ATP binding cassette (ABC) transporters. Both systems have similar Km values of approximately 1 mM. According to our estimations this low affinity appears nevertheless to be sufficient for the continuous vacuolar sequestration of ABA GE produced in the cytosol. We further demonstrate that two tested multispecific vacuolar ABCC type ABC transporters from Arabidopsis exhibit ABA GE transport activity when expressed in yeast (Saccharomyces cerevisiae) which also supports the involvement of ABC transporters in ABA GE uptake. Our findings suggest that the vacuolar ABA GE uptake is not mediated by specific but rather by several possibly multispecific transporters that are involved in the general vacuolar sequestration of conjugated metabolites.
- Published
- 2013
7. An ATP-binding cassette protein from grape berry (VvABCC1) transports glucosylated anthocyanins
- Author
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Francisco R, Regalado A, Agegeorges A, Burla B, Bassin B, Eisenach C, zarouk O, Chaves MM, Martinoia E, and Nagy R
- Subjects
carbohydrates (lipids) ,fungi ,food and beverages - Abstract
Accumulation of anthocyanins in the exocarp of red grapevine (Vitis vinifera) cultivars is one of several events that characterize the onset of grape berry ripening (véraison). Despite our thorough understanding of anthocyanin biosynthesis and regulation little is known about the molecular aspects of their transport. The participation of ATP binding cassette (ABC) proteins in vacuolar anthocyanin transport has long been a matter of debate. Here we present biochemical evidence that an ABC protein ABCC1 localizes to the tonoplast and is involved in the transport of glucosylated anthocyanidins. ABCC1 is expressed in the exocarp throughout berry development and ripening with a significant increase at véraison (i.e. the onset of ripening). Transport experiments using microsomes isolated from ABCC1 expressing yeast cells showed that ABCC1 transports malvidin 3 O glucoside. The transport strictly depends on the presence of GSH which is cotransported with the anthocyanins and is sensitive to inhibitors of ABC proteins. By exposing anthocyanin producing grapevine root cultures to buthionine sulphoximine which reduced GSH levels a decrease in anthocyanin concentration is observed. In conclusion we provide evidence that ABCC1 acts as an anthocyanin transporter that depends on GSH without the formation of an anthocyanin GSH conjugate.
- Published
- 2013
8. Malate transport by the vacuolar AtALMT6 channel in guard cells is subject to multiple regulation
- Author
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Meyer S, Scholz-Starke J, De Angeli A, Kovermann P, Burla B, Gambale F, Martinoia E, University of Zurich, and De Angeli, A
- Subjects
1307 Cell Biology ,10126 Department of Plant and Microbial Biology ,1311 Genetics ,fungi ,1110 Plant Science ,food and beverages ,580 Plants (Botany) - Abstract
Gas exchange in plants is controlled by guard cells, specialized cells acting as turgor pressure-driven valves. Malate is one of the major anions accumulated inside the vacuole during stomatal opening counteracting the positive charge of potassium. AtALMT6, a member of the aluminum-activated malate transporter family, is expressed in guard cells of leaves and stems as well as in flower organs of Arabidopsis thaliana. An AtALMT6-GFP fusion protein was targeted to the vacuolar membrane both in transient and stable expression systems. Patch-clamp experiments on vacuoles isolated from AtALMT6-GFP over-expressing Arabidopsis plants revealed large inward-rectifying malate currents only in the presence of micromolar cytosolic calcium concentrations. Further analyses showed that vacuolar pH and cytosolic malate regulate the threshold of activation of AtALMT6-mediated currents. The interplay of these two factors determines the AtALMT6 function as a malate influx or efflux channel depending on the tonoplast potential. Guard cell vacuoles isolated from Atalmt6 knock-out plants displayed reduced malate currents compared with wild-type vacuoles. This reduction, however, was not accompanied by phenotypic differences in the stomatal movements in knock-out plants, probably because of functional redundancy of malate transporters in guard cell vacuoles
- Published
- 2011
9. Functions of ABC transporters in plants
- Author
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Kretzschmar, T, Burla, B, Lee, Y, Martinoia, E, Nagy, R, University of Zurich, and Martinoia, E
- Subjects
1303 Biochemistry ,10126 Department of Plant and Microbial Biology ,1312 Molecular Biology ,580 Plants (Botany) - Published
- 2011
10. Reversal of hemochromatosis by apotransferrin in non-transfused and transfused Hbbth3/+ (heterozygous b1/b2 globin gene deletion) mice
- Author
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Gelderman, M. P., primary, Baek, J. H., additional, Yalamanoglu, A., additional, Puglia, M., additional, Vallelian, F., additional, Burla, B., additional, Vostal, J., additional, Schaer, D. J., additional, and Buehler, P. W., additional
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- 2015
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11. Expression analysis and functional characterization of the monosaccharide transporters, OsTMTs, involving vacuolar sugar transport in rice (Oryza sativa)
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Cho, J I, Burla, B, Lee, D W, Ryoo, N, Hong, S K, Kim, H B, Eom, J S, Choi, S B, Cho, M H, Bhoo, S H, Hahn, T R, Neuhaus, H E, Martinoia, E, Jeon, J S, and University of Zurich
- Subjects
10126 Department of Plant and Microbial Biology ,1110 Plant Science ,1314 Physiology ,580 Plants (Botany) - Published
- 2010
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12. Reduced soil respiration in gaps in logged lowland dipterocarp forests
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Saner, P, Lim, R, Burla, B, Scherer-Lorenzen, M, Hector, A, University of Zurich, and Saner, P
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10127 Institute of Evolutionary Biology and Environmental Studies ,Gap dynamics ,Soil ecology ,2308 Management, Monitoring, Policy and Law ,Borneo ,Tropics ,570 Life sciences ,biology ,590 Animals (Zoology) ,1107 Forestry ,Logged forest ,Carbon cycle ,2309 Nature and Landscape Conservation - Published
- 2009
13. Pheophytin pheophorbide hydrolase (pheophytinase) is involved in chlorophyll breakdown during leaf senescence in Arabidopsis
- Author
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Schelbert, S, Aubry, S, Burla, B, Agne, B, Kessler, F, Krupinska, K, Hörtensteiner, S, University of Zurich, and Hörtensteiner, S
- Subjects
1307 Cell Biology ,10126 Department of Plant and Microbial Biology ,1110 Plant Science ,580 Plants (Botany) - Published
- 2009
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14. The ABC transporter AtABCB14 is a malate importer and modulates stomatal response to CO2
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Lee, M, Choi, Y, Burla, B, Kim, Y Y, Jeon, B, Maeshima, M, Yoo, J Y, Martinoia, E, Lee, Y, University of Zurich, and Lee, Y
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1307 Cell Biology ,10126 Department of Plant and Microbial Biology ,580 Plants (Botany) - Published
- 2008
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15. Plant ABC Transporters
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Kong, J, Park, J, Choi, H, Burla, B, Kretschmar, T, Lee, Y, Martinoia, E, Kong, J, Park, J, Choi, H, Burla, B, Kretschmar, T, Lee, Y, and Martinoia, E
- Abstract
ABC transporters constitute one of the largest protein families found in all living organisms. ABC transporters are driven by ATP hydrolysis and can act as exporters as well as importers. The plant genome encodes for more than 100 ABC transporters, largely exceeding that of other organisms. In Arabidopsis, only 22 out of 130 have been functionally analyzed. They are localized in most membranes of a plant cell such as the plasma membrane, the tonoplast, chloroplasts, mitochondria and peroxisomes and fulfill a multitude of functions. Originally identified as transporters involved in detoxification processes, they have later been shown to be required for organ growth, plant nutrition, plant development, response to abiotic stresses, pathogen resistance and the interaction of the plant with its environment. To fulfill these roles they exhibit different substrate specifies by e.g. depositing surface lipids, accumulating phytate in seeds, and transporting the phytohormones auxin and abscisic acid. The aim of this review is to give an insight into the functions of plant ABC transporters and to show their importance for plant development and survival.
- Published
- 2011
16. Malate transport by the vacuolar AtALMT6 channel in guard cells is subject to multiple regulation
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Meyer, S, Scholz-Starke, J, De Angeli, A, Kovermann, P, Burla, B, Gambale, F, Martinoia, E, Meyer, S, Scholz-Starke, J, De Angeli, A, Kovermann, P, Burla, B, Gambale, F, and Martinoia, E
- Abstract
Gas exchange in plants is controlled by guard cells, specialized cells acting as turgor pressure-driven valves. Malate is one of the major anions accumulated inside the vacuole during stomatal opening counteracting the positive charge of potassium. AtALMT6, a member of the aluminum-activated malate transporter family, is expressed in guard cells of leaves and stems as well as in flower organs of Arabidopsis thaliana. An AtALMT6-GFP fusion protein was targeted to the vacuolar membrane both in transient and stable expression systems. Patch-clamp experiments on vacuoles isolated from AtALMT6-GFP over-expressing Arabidopsis plants revealed large inward-rectifying malate currents only in the presence of micromolar cytosolic calcium concentrations. Further analyses showed that vacuolar pH and cytosolic malate regulate the threshold of activation of AtALMT6-mediated currents. The interplay of these two factors determines the AtALMT6 function as a malate influx or efflux channel depending on the tonoplast potential. Guard cell vacuoles isolated from Atalmt6 knock-out plants displayed reduced malate currents compared with wild-type vacuoles. This reduction, however, was not accompanied by phenotypic differences in the stomatal movements in knock-out plants, probably because of functional redundancy of malate transporters in guard cell vacuoles.
- Published
- 2011
17. Plant ABC proteins - a unified nomenclature and updated inventory
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Verrier, P J, Bird, D, Burla, B, Dassa, E, Forestier, C, Geisler, M, Klein, M, Kolukisaoglu, U, Lee, Y, Martinoia, E, Murphy, A, Rea, P A, Samuels, L, Schulz, B, Spalding, E J, Yazaki, K, and Theodoulou, F L
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2. Zero hunger
18. Concordant inter-laboratory derived concentrations of ceramides in human plasma reference materials via authentic standards.
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Torta F, Hoffmann N, Burla B, Alecu I, Arita M, Bamba T, Bennett SAL, Bertrand-Michel J, Brügger B, Cala MP, Camacho-Muñoz D, Checa A, Chen M, Chocholoušková M, Cinel M, Chu-Van E, Colsch B, Coman C, Connell L, Sousa BC, Dickens AM, Fedorova M, Eiríksson FF, Gallart-Ayala H, Ghorasaini M, Giera M, Guan XL, Haid M, Hankemeier T, Harms A, Höring M, Holčapek M, Hornemann T, Hu C, Hülsmeier AJ, Huynh K, Jones CM, Ivanisevic J, Izumi Y, Köfeler HC, Lam SM, Lange M, Lee JC, Liebisch G, Lippa K, Lopez-Clavijo AF, Manzi M, Martinefski MR, Math RGH, Mayor S, Meikle PJ, Monge ME, Moon MH, Muralidharan S, Nicolaou A, Nguyen-Tran T, O'Donnell VB, Orešič M, Ramanathan A, Riols F, Saigusa D, Schock TB, Schwartz-Zimmermann H, Shui G, Singh M, Takahashi M, Thorsteinsdóttir M, Tomiyasu N, Tournadre A, Tsugawa H, Tyrrell VJ, van der Gugten G, Wakelam MO, Wheelock CE, Wolrab D, Xu G, Xu T, Bowden JA, Ekroos K, Ahrends R, and Wenk MR
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- Humans, Calibration, Mass Spectrometry methods, Lipidomics methods, Reproducibility of Results, Ceramides blood, Reference Standards, Laboratories standards
- Abstract
In this community effort, we compare measurements between 34 laboratories from 19 countries, utilizing mixtures of labelled authentic synthetic standards, to quantify by mass spectrometry four clinically used ceramide species in the NIST (National Institute of Standards and Technology) human blood plasma Standard Reference Material (SRM) 1950, as well as a set of candidate plasma reference materials (RM 8231). Participants either utilized a provided validated method and/or their method of choice. Mean concentration values, and intra- and inter-laboratory coefficients of variation (CV) were calculated using single-point and multi-point calibrations, respectively. These results are the most precise (intra-laboratory CVs ≤ 4.2%) and concordant (inter-laboratory CVs < 14%) community-derived absolute concentration values reported to date for four clinically used ceramides in the commonly analyzed SRM 1950. We demonstrate that calibration using authentic labelled standards dramatically reduces data variability. Furthermore, we show how the use of shared RM can correct systematic quantitative biases and help in harmonizing lipidomics. Collectively, the results from the present study provide a significant knowledge base for translation of lipidomic technologies to future clinical applications that might require the determination of reference intervals (RIs) in various human populations or might need to estimate reference change values (RCV), when analytical variability is a key factor for recall during multiple testing of individuals., (© 2024. The Author(s).)
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- 2024
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19. Plasma and platelet lipidome changes in Fabry disease.
- Author
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Burla B, Oh J, Nowak A, Piraud N, Meyer E, Mei D, Bendt AK, Studt JD, Frey BM, Torta F, Wenk MR, and Krayenbuehl PA
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- Humans, Male, Adult, Female, Middle Aged, Lipids blood, Young Adult, Fabry Disease blood, Fabry Disease diagnosis, Blood Platelets metabolism, Blood Platelets pathology, Lipidomics
- Abstract
Background: Fabry disease (FD) is an X-linked lysosomal storage disorder characterized by the progressive accumulation of globotriaosylceramide (Gb3) leading to systemic manifestations such as chronic kidney disease, cardiomyopathy, and stroke. There is still a need for novel markers for improved FD screening and prognosis. Moreover, the pathological mechanisms in FD, which also include systemic inflammation and fibrosis, are not yet fully understood., Methods: Plasma and platelets were obtained from 11 ERT (enzyme-replacement therapy)-treated symptomatic, 4 asymptomatic FD patients, and 13 healthy participants. A comprehensive targeted lipidomics analysis was conducted quantitating more than 550 lipid species., Results: Sphingadiene (18:2;O2)-containing sphingolipid species, including Gb3 and galabiosylceramide (Ga2), were significantly increased in FD patients. Plasma levels of lyso-dihexosylceramides, sphingoid base 1-phosphates (S1P), and GM3 ganglioside were also altered in FD patients, as well as specific plasma ceramide ratios used in cardiovascular disease risk prediction. Gb3 did not increase in patients' platelets but displayed a high inter-individual variability in patients and healthy participants. Platelets accumulated, however, lyso-Gb3, acylcarnitines, C16:0-sphingolipids, and S1P., Conclusions: This study identified lipidome changes in plasma and platelets from FD patients, a possible involvement of platelets in FD, and potential new markers for screening and monitoring of this disease., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 The Authors. Published by Elsevier B.V. All rights reserved.)
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- 2024
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20. Sphingolipid Analysis in Clinical Research.
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Oh J, Burla B, Muralidharan S, Wenk MR, and Torta F
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- Humans, Chromatography, Liquid methods, Mass Spectrometry methods, Sphingolipids metabolism, Sphingolipids blood, Lipidomics methods
- Abstract
Sphingolipids are the most diverse class of lipids due to the numerous variations in their structural components. This diversity is also reflected in their extremely different functions. Sphingolipids are not only constituents of cell membranes but have emerged as key signaling molecules involved in a variety of cellular functions, such as cell growth and differentiation, proliferation and apoptotic cell death. Lipidomic analyses in clinical research have identified pathways and products of sphingolipid metabolism that are altered in several human pathologies. In this article, we describe how to properly design a lipidomic experiment in clinical research, how to handle plasma and serum samples for this purpose, and how to measure sphingolipids using liquid chromatography-mass spectrometry., (© 2025. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.)
- Published
- 2025
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21. Effects of wolfberry ( Lycium barbarum ) consumption on the human plasma lipidome and its association with cardiovascular disease risk factors: a randomized controlled trial of middle-aged and older adults.
- Author
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Toh DWK, Zhou H, Cazenave-Gassiot A, Choi H, Burla B, Bendt AK, Wenk MR, Ling LH, and Kim JE
- Abstract
Background: Long-term wolfberry intake as part of a healthy dietary pattern was recognized to have beneficial vascular outcomes. Characterization of the plasma lipidome may further provide comprehensive insights into pathways underlying these cardiovascular protective effects., Objective: We analyzed the plasma lipidome of subjects who adhered to a healthy dietary pattern either with or without wolfberry and investigated the associations between the plasma lipidomic profile and cardiovascular health-related indicators., Methods: In this 16-week, parallel design, randomized controlled trial, middle-aged and older adults ( n = 41) were provided dietary counseling and assigned to either consume or not consume 15 g of wolfberry daily. At baseline and post-intervention, plasma lipidomics was assayed, and its relationships with classical CVD risk factors, vascular health, oxidant burden, carotenoids status, body composition, and anthropometry were examined., Results: From the plasma lipidome, 427 lipid species from 26 sub-classes were quantified. In the wolfberry and control groups, significant changes were prominent for 27 and 42 lipid species, respectively ( P < 0.05 with > 0.2-fold change). Fold changes for seven lipid species were also markedly different between the two groups. Examining the relationships between the plasma lipidome and CVD-related risk factors, total cholesterol revealed a marked positive correlation with 13 ceramide species, while HDL-cholesterol which was notably increased with wolfberry consumption showed a positive correlation with 10 phosphatidylcholine species. Oxidant burden, as represented by plasma 8-isoprostanes, was also inversely associated with lipidomic triglycerides and ether-triglycerides (41 species) and directly associated with hexosylceramides (eight species) and sphingomyelins (six species). There were no differential associations with CVD risk detected between groups., Conclusion: Characteristic alterations to the plasma lipidome were observed with healthy dietary pattern adherence and wolfberry consumption. An examination of these fluctuations suggests potential biochemical mechanisms that may mediate the antioxidant and cardiovascular protective effects of healthy dietary pattern adherence and wolfberry intake. This study was registered at clinicaltrials.gov as NCT0353584., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2024 Toh, Zhou, Cazenave-Gassiot, Choi, Burla, Bendt, Wenk, Ling and Kim.)
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- 2024
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22. An integrated signature of extracellular matrix proteins and a diastolic function imaging parameter predicts post-MI long-term outcomes.
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Koh HWL, Pilbrow AP, Tan SH, Zhao Q, Benke PI, Burla B, Torta F, Pickering JW, Troughton R, Pemberton C, Soo WM, Ling LH, Doughty RN, Choi H, Wenk MR, Richards AM, and Chan MY
- Abstract
Background: Patients suffering from acute myocardial infarction (AMI) are at risk of secondary outcomes including major adverse cardiovascular events (MACE) and heart failure (HF). Comprehensive molecular phenotyping and cardiac imaging during the post-discharge time window may provide cues for risk stratification for the outcomes., Materials and Methods: In a prospective AMI cohort in New Zealand ( N = 464), we measured plasma proteins and lipids 30 days after hospital discharge and inferred a unified partial correlation network with echocardiographic variables and established clinical biomarkers (creatinine, c-reactive protein, cardiac troponin I and natriuretic peptides). Using a network-based data integration approach (iOmicsPASS+), we identified predictive signatures of long-term secondary outcomes based on plasma protein, lipid, imaging markers and clinical biomarkers and assessed the prognostic potential in an independent cohort from Singapore ( N = 190)., Results: The post-discharge levels of plasma proteins and lipids showed strong correlations within each molecular type, reflecting concerted homeostatic regulation after primary MI events. However, the two molecular types were largely independent with distinct correlation structures with established prognostic imaging parameters and clinical biomarkers. To deal with massively correlated predictive features, we used iOmicsPASS + to identify subnetwork signatures of 211 and 189 data features (nodes) predictive of MACE and HF events, respectively (160 overlapping). The predictive features were primarily imaging parameters, including left ventricular and atrial parameters, tissue Doppler parameters, and proteins involved in extracellular matrix (ECM) organization, cell differentiation, chemotaxis, and inflammation. The network signatures contained plasma protein pairs with area-under-the-curve (AUC) values up to 0.74 for HF prediction in the validation cohort, but the pair of NT-proBNP and fibulin-3 ( EFEMP1 ) was the best predictor (AUC = 0.80). This suggests that there were a handful of plasma proteins with mechanistic and functional roles in predisposing patients to the secondary outcomes, although they may be weaker prognostic markers than natriuretic peptides individually. Among those, the diastolic function parameter (E/e' - an indicator of left ventricular filling pressure) and two ECM proteins, EFEMP1 and follistatin-like 3 ( FSTL3 ) showed comparable performance to NT-proBNP and outperformed left ventricular measures as benchmark prognostic factors for post-MI HF., Conclusion: Post-discharge levels of E/e', EFEMP1 and FSTL3 are promising complementary markers of secondary adverse outcomes in AMI patients., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (© 2023 Koh, Pilbrow, Tan, Zhao, Benke, Burla, Torta, Pickering, Troughton, Pemberton, Soo, Ling, Doughty, Choi, Wenk, Richards and Chan.)
- Published
- 2023
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23. Automated detection of dolphin whistles with convolutional networks and transfer learning.
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Nur Korkmaz B, Diamant R, Danino G, and Testolin A
- Abstract
Effective conservation of maritime environments and wildlife management of endangered species require the implementation of efficient, accurate and scalable solutions for environmental monitoring. Ecoacoustics offers the advantages of non-invasive, long-duration sampling of environmental sounds and has the potential to become the reference tool for biodiversity surveying. However, the analysis and interpretation of acoustic data is a time-consuming process that often requires a great amount of human supervision. This issue might be tackled by exploiting modern techniques for automatic audio signal analysis, which have recently achieved impressive performance thanks to the advances in deep learning research. In this paper we show that convolutional neural networks can indeed significantly outperform traditional automatic methods in a challenging detection task: identification of dolphin whistles from underwater audio recordings. The proposed system can detect signals even in the presence of ambient noise, at the same time consistently reducing the likelihood of producing false positives and false negatives. Our results further support the adoption of artificial intelligence technology to improve the automatic monitoring of marine ecosystems., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2023 Nur Korkmaz, Diamant, Danino and Testolin.)
- Published
- 2023
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24. Evaluation of Normalization Approaches for Quantitative Analysis of Bile Acids in Human Feces.
- Author
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Schött HF, Chua EWL, Mir SA, Burla B, Bendt AK, and Wenk MR
- Abstract
Quantitative analysis of bile acids in human feces can potentially help to better understand the influence of the gut microbiome and diet on human health. Feces is a highly heterogeneous sample matrix, mainly consisting of water and indigestible solid material (as plant fibers) that show high inter-individual variability. To compare bile acid concentrations among different individuals, a reliable normalization approach is needed. Here, we compared the impact of three normalization approaches, namely sample wet weight, dry weight, and protein concentration, on the absolute concentrations of fecal bile acids. Bile acid concentrations were determined in 70 feces samples from healthy humans. Our data show that bile acid concentrations normalized by the three different approaches are substantially different for each individual sample. Fecal bile acid concentrations normalized by wet weight show the narrowest distribution. Therefore, our analysis will provide the basis for the selection of a suitable normalization approach for the quantitative analysis of bile acids in feces.
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- 2022
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25. Population-based plasma lipidomics reveals developmental changes in metabolism and signatures of obesity risk: a mother-offspring cohort study.
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Mir SA, Chen L, Burugupalli S, Burla B, Ji S, Smith AAT, Narasimhan K, Ramasamy A, Tan KM, Huynh K, Giles C, Mei D, Wong G, Yap F, Tan KH, Collier F, Saffery R, Vuillermin P, Bendt AK, Burgner D, Ponsonby AL, Lee YS, Chong YS, Gluckman PD, Eriksson JG, Meikle PJ, Wenk MR, and Karnani N
- Subjects
- Birth Weight, Body Mass Index, Chromatography, Liquid, Cohort Studies, Female, Humans, Obesity complications, Pregnancy, Tandem Mass Spectrometry, Triglycerides, Lipidomics, Mothers
- Abstract
Background: Lipids play a vital role in health and disease, but changes to their circulating levels and the link with obesity remain poorly characterized in expecting mothers and their offspring in early childhood., Methods: LC-MS/MS-based quantitation of 480 lipid species was performed on 2491 plasma samples collected at 4 time points in the mother-offspring Asian cohort GUSTO (Growing Up in Singapore Towards healthy Outcomes). These 4 time points constituted samples collected from mothers at 26-28 weeks of gestation (n=752) and 4-5 years postpartum (n=650), and their offspring at birth (n=751) and 6 years of age (n=338). Linear regression models were used to identify the pregnancy and developmental age-specific variations in the plasma lipidomic profiles, and their association with obesity risk. An independent birth cohort (n=1935), the Barwon Infant Study (BIS), comprising mother-offspring dyads of Caucasian origin was used for validation., Results: Levels of 36% of the profiled lipids were significantly higher (absolute fold change > 1.5 and P
adj < 0.05) in antenatal maternal circulation as compared to the postnatal phase, with phosphatidylethanolamine levels changing the most. Compared to antenatal maternal lipids, cord blood showed lower concentrations of most lipid species (79%) except lysophospholipids and acylcarnitines. Changes in lipid concentrations from birth to 6 years of age were much higher in magnitude (log2 FC=-2.10 to 6.25) than the changes observed between a 6-year-old child and an adult (postnatal mother) (log2 FC=-0.68 to 1.18). Associations of cord blood lipidomic profiles with birth weight displayed distinct trends compared to the lipidomic profiles associated with child BMI at 6 years. Comparison of the results between the child and adult BMI identified similarities in association with consistent trends (R2 =0.75). However, large number of lipids were associated with BMI in adults (67%) compared to the children (29%). Pre-pregnancy BMI was specifically associated with decrease in the levels of phospholipids, sphingomyelin, and several triacylglycerol species in pregnancy., Conclusions: In summary, our study provides a detailed landscape of the in utero lipid environment provided by the gestating mother to the growing fetus, and the magnitude of changes in plasma lipidomic profiles from birth to early childhood. We identified the effects of adiposity on the circulating lipid levels in pregnant and non-pregnant women as well as offspring at birth and at 6 years of age. Additionally, the pediatric vs maternal overlap of the circulating lipid phenotype of obesity risk provides intergenerational insights and early opportunities to track and intervene the onset of metabolic adversities., Clinical Trial Registration: This birth cohort is a prospective observational study, which was registered on 1 July 2010 under the identifier NCT01174875 ., (© 2022. The Author(s).)- Published
- 2022
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26. Immunolipidomics Reveals a Globoside Network During the Resolution of Pro-Inflammatory Response in Human Macrophages.
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Muralidharan S, Torta F, Lin MK, Olona A, Bagnati M, Moreno-Moral A, Ko JH, Ji S, Burla B, Wenk MR, Rodrigues HG, Petretto E, and Behmoaras J
- Subjects
- Chromatography, Liquid, Humans, Tandem Mass Spectrometry, Globosides, Lipopolysaccharides, Macrophages immunology
- Abstract
Toll-like receptor 4 (TLR4)-mediated changes in macrophages reshape intracellular lipid pools to coordinate an effective innate immune response. Although this has been previously well-studied in different model systems, it remains incompletely understood in primary human macrophages. Here we report time-dependent lipidomic and transcriptomic responses to lipopolysaccharide (LPS) in primary human macrophages from healthy donors. We grouped the variation of ~200 individual lipid species measured by LC-MS/MS into eight temporal clusters. Among all other lipids, glycosphingolipids (glycoSP) and cholesteryl esters (CE) showed a sharp increase during the resolution phase (between 8h or 16h post LPS). GlycoSP, belonging to the globoside family (Gb3 and Gb4), showed the greatest inter-individual variability among all lipids quantified. Integrative network analysis between GlycoSP/CE levels and genome-wide transcripts, identified Gb4 d18:1/16:0 and CE 20:4 association with subnetworks enriched for T cell receptor signaling ( PDCD1 , CD86 , PTPRC , CD247 , IFNG ) and DC-SIGN signaling ( RAF1 , CD209 ), respectively. Our findings reveal Gb3 and Gb4 globosides as sphingolipids associated with the resolution phase of inflammatory response in human macrophages., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Muralidharan, Torta, Lin, Olona, Bagnati, Moreno-Moral, Ko, Ji, Burla, Wenk, Rodrigues, Petretto and Behmoaras.)
- Published
- 2022
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27. Serum Lipidome Signatures of Dogs with Different Endocrinopathies Associated with Hyperlipidemia.
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Sieber-Ruckstuhl NS, Tham WK, Baumgartner F, Selva JJ, Wenk MR, Burla B, and Boretti FS
- Abstract
Hyperlipidemia (hypertriglyceridemia, hypercholesterolemia) is a common finding in human and veterinary patients with endocrinopathies (e.g., hypothyroidism and hypercortisolism (Cushing's syndrome; CS)). Despite emerging use of lipidomics technology in medicine, the lipid profiles of these endocrinopathies have not been evaluated and characterized in dogs. The aim of this study was to compare the serum lipidomes of dogs with naturally occurring CS or hypothyroidism with those of healthy dogs. Serum samples from 39 dogs with CS, 45 dogs with hypothyroidism, and 10 healthy beagle dogs were analyzed using a targeted lipidomics approach with liquid chromatography-mass spectrometry. There were significant differences between the lipidomes of dogs with CS, hypothyroidism, and the healthy dogs. The most significant changes were found in the lysophosphatidylcholines, lysophosphatidylethanolamines, lysophosphatidylinositols, phosphatidylcholines, phosphatidylethanolamines, phosphatidylglycerols, ceramides, and sphingosine 1-phosphates. Lipid alterations were especially pronounced in dogs with hypothyroidism. Several changes suggested a more atherogenic lipid profile in dogs with HT than in dogs with CS. In this study, we found so far unknown effects of naturally occurring hypothyroidism and CS on lipid metabolism in dogs. Our findings provide starting points to further examine differences in occurrence of atherosclerotic lesion formation between the two diseases.
- Published
- 2022
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28. Variability of the Plasma Lipidome and Subclinical Coronary Atherosclerosis.
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Tan SH, Koh HWL, Chua JY, Burla B, Ong CC, Teo LSL, Yang X, Benke PI, Choi H, Torta F, Richards AM, Wenk MR, and Chan MY
- Subjects
- Adult, Aged, Asymptomatic Diseases, Biomarkers blood, Computed Tomography Angiography, Coronary Angiography, Coronary Artery Disease diagnostic imaging, Female, Humans, Longitudinal Studies, Male, Middle Aged, Plaque, Atherosclerotic, Time Factors, Coronary Artery Disease blood, Lipidomics, Lipids blood
- Abstract
Objective: While the risk of acute coronary events has been associated with biological variability of circulating cholesterol, the association with variability of other atherogenic lipids remains less understood. We evaluated the longitudinal variability of 284 lipids and investigated their association with asymptomatic coronary atherosclerosis. Approach and Results: Circulating lipids were extracted from fasting blood samples of 83 community-sampled symptom-free participants (age 41-75 years), collected longitudinally over 6 months. Three types of coronary plaque volume (calcified, lipid-rich, and fibrotic) were quantified using computed tomography coronary angiogram. We first deconvoluted between-subject (CV
g ) and within-subject (CVw ) lipid variabilities. We then tested whether the mean lipid abundance was different across groups categorized by Framingham risk score and plaques phenotypes (lipid-rich, fibrotic, and calcified). Finally, we investigated whether visit-to-visit variability of each lipid was associated with plaque burden. Most lipids (72.5%) exhibited higher CVg than CVw . Among the lipids (n=145) with 1.2-fold higher CVg than CVw , 26 species including glycerides and ceramides were significantly associated with Framingham risk score and the 3 plaque phenotypes (false discovery rate <0.05). In an exploratory analysis of person-specific visit-to-visit variability without multiple testing correction, high variability of 3 lysophospholipids (lysophosphatidylethanolamines 16:0, 18:0, and lysophosphatidylcholine O-18:1) was associated with lipid-rich and fibrotic (noncalcified) plaque volume while high variability of diacylglycerol 18:1_20:0, triacylglycerols 52:2, 52:3, and 52:4, ceramide d18:0/20:0, dihexosylceramide d18:1/16:0, and sphingomyelin 36:3 was associated with calcified plaque volume., Conclusions: High person-specific longitudinal variation of specific nonsterol lipids is associated with the burden of subclinical coronary atherosclerosis. Larger studies are needed to confirm these exploratory findings.- Published
- 2022
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29. Lipidomic Analysis of Archival Pathology Specimens Identifies Altered Lipid Signatures in Ovarian Clear Cell Carcinoma.
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Mir SA, Wong SBJ, Narasimhan K, Esther CWL, Ji S, Burla B, Wenk MR, Tan DSP, and Bendt AK
- Abstract
Cancer metabolism is associated with the enhanced lipogenesis required for rapid growth and proliferation. However, the magnitude of dysregulation of diverse lipid species still requires significant characterization, particularly in ovarian clear cell carcinoma (OCCC). Here, we have implemented a robust sample preparation workflow together with targeted LC-MS/MS to identify the lipidomic changes in formalin-fixed paraffin-embedded specimens from OCCC compared to tumor-free ovarian tissue. We quantitated 340 lipid species, representing 28 lipid classes. We observed differential regulation of diverse lipid species belonging to several glycerophospholipid classes and trihexosylceramide. A number of unsaturated lipid species were increased in OCCC, whereas saturated lipid species showed a decrease in OCCC compared to the controls. We also carried out total fatty acid analysis and observed an increase in the levels of several unsaturated fatty acids with a concomitant increase in the index of stearoyl-CoA desaturase (SCD) in OCCC. We confirmed the upregulation of SCD (the rate-limiting enzyme for the synthesis of monounsaturated fatty acids) by immunohistochemistry (IHC) assays. Hence, by carrying out a mass spectrometry analysis of archival tissue samples, we were able to provide insights into lipidomic alterations in OCCC.
- Published
- 2021
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30. A reference map of sphingolipids in murine tissues.
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Muralidharan S, Shimobayashi M, Ji S, Burla B, Hall MN, Wenk MR, and Torta F
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- Animals, Cluster Analysis, Diet, High-Fat, Female, Lipidomics, Lysophospholipids metabolism, Male, Mice, Inbred C57BL, Sex Characteristics, Sphingolipids blood, Sphingosine analogs & derivatives, Sphingosine metabolism, Mice, Organ Specificity, Sphingolipids metabolism
- Abstract
Sphingolipids (SPs) have both a structural role in the cell membranes and a signaling function that regulates many cellular processes. The enormous structural diversity and low abundance of many SPs pose a challenge for their identification and quantification. Recent advances in lipidomics, in particular liquid chromatography (LC) coupled with mass spectrometry (MS), provide methods to detect and quantify many low-abundant SP species reliably. Here we use LC-MS to compile a "murine sphingolipid atlas," containing the qualitative and quantitative distribution of 114 SPs in 21 tissues of a widely utilized wild-type laboratory mouse strain (C57BL/6). We report tissue-specific SP fingerprints, as well as sex-specific differences in the same tissue. This is a comprehensive, quantitative sphingolipidomic map of mammalian tissues collected in a systematic fashion. It will complement other tissue compendia for interrogation into the role of SP in mammalian health and disease., Competing Interests: Declaration of interests The authors declare no competing interests., (Copyright © 2021 The Authors. Published by Elsevier Inc. All rights reserved.)
- Published
- 2021
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31. LICAR: An Application for Isotopic Correction of Targeted Lipidomic Data Acquired with Class-Based Chromatographic Separations Using Multiple Reaction Monitoring.
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Gao L, Ji S, Burla B, Wenk MR, Torta F, and Cazenave-Gassiot A
- Subjects
- Chromatography, Liquid, Humans, Hydrophobic and Hydrophilic Interactions, Lipids, Chromatography, Supercritical Fluid, Lipidomics
- Abstract
Lipidomics is developing as an important area in biomedical and clinical research. Reliable quantification of lipid species is required for clinical translation of lipidomic studies. Hydrophilic interaction chromatography (HILIC), normal-phase liquid chromatography (NPLC), and supercritical fluid chromatography (SFC) are commonly used techniques in lipidomics and provide class-based separation of lipids. While co-elution of lipid species and their internal standards is an advantage for accurate quantification, it leads to isotopic overlap between species of the same lipid class. In shotgun lipidomics, isotopic correction is typically done based on elemental formulas of precursor ions. In multiple reaction monitoring (MRM) analyses, however, this approach should not be used, as the overall contribution of heavy isotopes to the MRM transitions' intensities depends on their location in the molecule with respect to the fragmentation pattern. We present an algorithm, provided in the R programming language, for isotopic correction in class-based separation using MRM, extracting relevant structural information from MRM transitions to apply adequate isotopic correction factors. Using standards, we show that our algorithm accurately estimates the isotopic contribution of isotopologues to MRM transitions' measured intensities. Using human plasma as an example, we demonstrate the necessity of adequate isotopic correction for accurate quantitation of lipids measured by MRM with class-based chromatographic separation. We show that over a third of the measured phosphatidylcholine species had their intensity corrected by more than 10%. This isotopic correction algorithm and R-implemented application enable a more accurate quantification of lipids in class-based separation-MRM, a prerequisite for successful translation of lipidomic applications.
- Published
- 2021
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32. SmartPeak Automates Targeted and Quantitative Metabolomics Data Processing.
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Kutuzova S, Colaianni P, Röst H, Sachsenberg T, Alka O, Kohlbacher O, Burla B, Torta F, Schrübbers L, Kristensen M, Nielsen L, Herrgård MJ, and McCloskey D
- Subjects
- Automation, Chromatography, Liquid, Electrophoresis, Capillary, Tandem Mass Spectrometry, Time Factors, Electronic Data Processing methods, Metabolomics methods
- Abstract
Technological advances in high-resolution mass spectrometry (MS) vastly increased the number of samples that can be processed in a life science experiment, as well as volume and complexity of the generated data. To address the bottleneck of high-throughput data processing, we present SmartPeak (https://github.com/AutoFlowResearch/SmartPeak), an application that encapsulates advanced algorithms to enable fast, accurate, and automated processing of capillary electrophoresis-, gas chromatography-, and liquid chromatography (LC)-MS(/MS) data and high-pressure LC data for targeted and semitargeted metabolomics, lipidomics, and fluxomics experiments. The application allows for an approximate 100-fold reduction in the data processing time compared to manual processing while enhancing quality and reproducibility of the results.
- Published
- 2020
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33. Impact of ion suppression by sample cap liners in lipidomics.
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Benke PI, Burla B, Ekroos K, Wenk MR, and Torta F
- Subjects
- Chromatography, Liquid, Humans, Lipids, Mass Spectrometry, Lipidomics, Metabolomics
- Abstract
Contamination from the polymeric material released by vial caps used for sample introduction in liquid chromatography can significantly affect the signal of the analyte of interest. In particular, repeated injections from the same sample vial can enhance this suppressing effect. Multiple injections of the same sample are often used in metabolomics and lipidomics during routine analyses. Here we demonstrate how the presence of contaminant polymers, originating from the vial closures, significantly influences the estimation of the relative amount of endogenous lipids in human plasma. Furthermore, this can negatively impact other operations in mass spectrometric analysis, such as instrument equilibration and tuning or the common use of technical replicates to improve confidence in data interpretation. Our observations provide critical information on how to improve future analyses through the use of appropriate vial caps, solvents, chromatographic separations and equipment., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper. Acknowledgements Work in our laboratory is supported by grants from the National University of Singapore via the Life Sciences Institute (LSI), the National Research Foundation (NRF, NRFI2015-05 and NRFSBP-P4), the NRF and A∗STAR IAF-ICP I1901E0040, NUS iHealthtech Precision Medicine and Personalised Therapeutics., (Copyright © 2020 Elsevier B.V. All rights reserved.)
- Published
- 2020
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34. Simple Targeted Assays for Metabolic Pathways and Signaling: A Powerful Tool for Targeted Proteomics.
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Kopczynski D, Hentschel A, Coman C, Schebb NH, Hornemann T, Mashek DG, Hartung NM, Shevchuk O, Schött HF, Lorenz K, Torta F, Burla B, Zahedi RP, Sickmann A, Kreutz MR, Ejsing CS, Medenbach J, and Ahrends R
- Subjects
- Animals, Chromatography, High Pressure Liquid, Databases, Protein, Insulin metabolism, Mice, Peptides analysis, Tandem Mass Spectrometry, Metabolic Networks and Pathways genetics, Proteomics methods, Signal Transduction genetics
- Abstract
We introduce STAMPS, a pathway-centric web service for the development of targeted proteomics assays. STAMPS guides the user by providing several intuitive interfaces for a rapid and simplified method design. Applying our curated framework to signaling and metabolic pathways, we reduced the average assay development time by a factor of ∼150 and revealed that the insulin signaling is actively controlled by protein abundance changes in insulin-sensitive and -resistance states. Although at the current state STAMPS primarily contains mouse data, it was designed for easy extension with additional organisms.
- Published
- 2020
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35. LipidCreator workbench to probe the lipidomic landscape.
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Peng B, Kopczynski D, Pratt BS, Ejsing CS, Burla B, Hermansson M, Benke PI, Tan SH, Chan MY, Torta F, Schwudke D, Meckelmann SW, Coman C, Schmitz OJ, MacLean B, Manke MC, Borst O, Wenk MR, Hoffmann N, and Ahrends R
- Subjects
- Adult, Blood Platelets metabolism, Calibration, Female, Humans, Lipids blood, Lipids chemistry, Male, Platelet Activation, Probability, Reproducibility of Results, Signal Transduction, Young Adult, Lipidomics methods, Software
- Abstract
Mass spectrometry (MS)-based targeted lipidomics enables the robust quantification of selected lipids under various biological conditions but comprehensive software tools to support such analyses are lacking. Here we present LipidCreator, a software that fully supports targeted lipidomics assay development. LipidCreator offers a comprehensive framework to compute MS/MS fragment masses for over 60 lipid classes. LipidCreator provides all functionalities needed to define fragments, manage stable isotope labeling, optimize collision energy and generate in silico spectral libraries. We validate LipidCreator assays computationally and analytically and prove that it is capable to generate large targeted experiments to analyze blood and to dissect lipid-signaling pathways such as in human platelets.
- Published
- 2020
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36. Dual mass spectrometry as a tool to improve annotation and quantification in targeted plasma lipidomics.
- Author
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Gao L, Cazenave-Gassiot A, Burla B, Wenk MR, and Torta F
- Subjects
- Chromatography, Liquid, Humans, Lipids chemistry, Molecular Structure, Lipidomics, Lipids blood, Tandem Mass Spectrometry
- Abstract
Introduction: High quality data, based on reliable quantification and clear identification of the reported lipid species, are required for the clinical translation of human plasma lipidomic studies., Objective: Lipid quantification can be efficiently performed on triple quadrupole (QqQ) mass spectrometers in targeted multiple reaction monitoring (MRM) mode. However, a series of issues can be encountered when aiming at unambiguous identification and accurate quantification, including (i) resolving peaks of polyunsaturated species, (ii) discriminating between plasmanyl-, plasmenyl- and odd chain species and (iii) resolving the isotopic overlap between co-eluting lipid species., Methods: As a practical tool to improve the quality of targeted lipidomics studies, we applied a Dual MS platform by simultaneously coupling a reversed-phase liquid chromatography separation to a QqQ and a quadrupole-time of flight (Q-ToF) mass spectrometers. In one single experiment, this platform allows to correctly identify, by high-resolution MS and MS/MS, the peaks that are quantified by MRM., Results: As proof of concept, we applied the platform on glycerophosphocholines (GPCs) and sphingomyelins (SMs), which are highly abundant in human plasma and play crucial roles in various physiological functions. Our results demonstrated that Dual MS could provide a higher level of confidence in the identification and quantification of GPCs and SMs in human plasma. The same approach can also be applied to improve the study of other lipid classes and expanded for the identification of novel lipid molecular species., Conclusions: This methodology might have a great potential to achieve a better specificity in the quantification of lipids by targeted lipidomics in high-throughput studies.
- Published
- 2020
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37. Shared reference materials harmonize lipidomics across MS-based detection platforms and laboratories.
- Author
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Triebl A, Burla B, Selvalatchmanan J, Oh J, Tan SH, Chan MY, Mellet NA, Meikle PJ, Torta F, and Wenk MR
- Subjects
- Adult, Female, Healthy Volunteers, Humans, Male, Reference Standards, Young Adult, Lipidomics standards, Lipids blood, Mass Spectrometry
- Abstract
Quantitative MS of human plasma lipids is a promising technology for translation into clinical applications. Current MS-based lipidomic methods rely on either direct infusion (DI) or chromatographic lipid separation methods (including reversed phase and hydrophilic interaction LC). However, the use of lipid markers in laboratory medicine is limited by the lack of reference values, largely because of considerable differences in the concentrations measured by different laboratories worldwide. These inconsistencies can be explained by the use of different sample preparation protocols, method-specific calibration procedures, and other experimental and data-reporting parameters, even when using identical starting materials. Here, we systematically investigated the roles of some of these variables in multiple approaches to lipid analysis of plasma samples from healthy adults by considering: 1 ) different sample introduction methods (separation vs. DI methods); 2 ) different MS instruments; and 3 ) between-laboratory differences in comparable analytical platforms. Each of these experimental variables resulted in different quantitative results, even with the inclusion of isotope-labeled internal standards for individual lipid classes. We demonstrated that appropriate normalization to commonly available reference samples (i.e., "shared references") can largely correct for these systematic method-specific quantitative biases. Thus, to harmonize data in the field of lipidomics, in-house long-term references should be complemented by a commonly available shared reference sample, such as NIST SRM 1950, in the case of human plasma., (Copyright © 2020 Triebl et al. Published by The American Society for Biochemistry and Molecular Biology, Inc.)
- Published
- 2020
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38. Serum lipidome analysis of healthy beagle dogs receiving different diets.
- Author
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Boretti FS, Burla B, Deuel J, Gao L, Wenk MR, Liesegang A, and Sieber-Ruckstuhl NS
- Subjects
- Animals, Cholesterol blood, Chromatography, High Pressure Liquid, Dogs, Fish Oils administration & dosage, Linseed Oil administration & dosage, Lysophospholipids blood, Male, Mass Spectrometry, Principal Component Analysis, Sphingosine analogs & derivatives, Sphingosine blood, Triglycerides blood, Diet veterinary, Lipids blood
- Abstract
Introduction: Food and dietary ingredients have significant effects on metabolism and health., Objective: To evaluate whether and how different diets affected the serum lipidomic profile of dogs., Methods: Sixteen healthy beagles were fed a commercial dry diet for 3 months (control diet). After an overnight fasting period, a blood sample was taken for serum lipidomic profile analysis, and each dog was then randomly assigned to one of two groups. Group 1 was fed a commercial diet (Diet 1) and group 2 was fed a self-made, balanced diet supplemented with linseed oil and salmon oil (Diet 2) for 3 months. After an overnight fasting period, a blood sample was taken from each dog. Serum cholesterol and triacylglycerol analyses were performed and the serum lipidomic profiles were analyzed using targeted liquid chromatography-mass spectrometry., Results: Dogs fed the supplemented self-made diet (Diet 2) had significantly higher omega-3 fatty acid-containing lipids species and significantly lower saturated and mono- and di-unsaturated lipid species. Concentrations of sphingosine 1-phosphate species S1P d16:1 and S1P d17:1 were significantly increased after feeding Diet 2., Conclusion: This study found that different diets had significant effects on the dog's serum lipidomic profile. Therefore, in studies that include lipidomic analyses, diet should be included as a confounding factor.
- Published
- 2019
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39. A T164S mutation in the dengue virus NS1 protein is associated with greater disease severity in mice.
- Author
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Chan KWK, Watanabe S, Jin JY, Pompon J, Teng D, Alonso S, Vijaykrishna D, Halstead SB, Marzinek JK, Bond PJ, Burla B, Torta F, Wenk MR, Ooi EE, and Vasudevan SG
- Subjects
- Amino Acid Sequence, Animals, Cell Line, Conserved Sequence, Culicidae virology, Gene Expression Regulation, Inflammation genetics, Kinetics, Leukocytes, Mononuclear virology, Mice, Models, Molecular, Mutant Proteins chemistry, Phylogeny, Protein Multimerization, Protein Stability, Viral Nonstructural Proteins chemistry, Virus Replication, Dengue pathology, Dengue virology, Dengue Virus genetics, Mutation genetics, Severity of Illness Index, Viral Nonstructural Proteins genetics
- Abstract
Dengue viruses cause severe and sudden human epidemics worldwide. The secreted form of the nonstructural protein 1 (sNS1) of dengue virus causes vascular leakage, a hallmark of severe dengue disease. Here, we reverse engineered the T164S mutation of NS1, associated with the severity of dengue epidemics in the Americas, into a dengue virus serotype 2 mildly infectious strain. The T164S mutant virus decreased infectious virus production and increased sNS1 production in mammalian cell lines and human peripheral blood mononuclear cells (PBMCs) without affecting viral RNA replication. Gene expression profiling of 268 inflammation-associated human genes revealed up-regulation of genes induced in response to vascular leakage. Infection of the mosquito vector Aedes aegypti with the T164S mutant virus resulted in increased viral load in the mosquito midgut and higher sNS1 production compared to wild-type virus infection. Infection of type 1 and 2 interferon receptor-deficient AG129 mice with the T164S mutant virus resulted in severe disease coupled with increased complement activation, tissue inflammation, and more rapid mortality compared to AG129 mice infected with wild-type virus. Molecular dynamics simulations predicted that mutant sNS1 formed stable dimers similar to the wild-type protein, whereas the hexameric mutant sNS1 was predicted to be unstable. Immunoaffinity-purified sNS1 from T164S mutant virus-infected mammalian cells was associated with different lipid classes compared to wild-type sNS1. Treatment of human PBMCs with sNS1 purified from T164S mutant virus resulted in a twofold higher production of proinflammatory cytokines, suggesting a mechanism for how mutant sNS1 may cause more severe dengue disease., (Copyright © 2019 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.)
- Published
- 2019
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40. Changes in the Canine Plasma Lipidome after Short- and Long-Term Excess Glucocorticoid Exposure.
- Author
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Sieber-Ruckstuhl NS, Burla B, Spoerel S, Schmid F, Venzin C, Cazenave-Gassiot A, Bendt AK, Torta F, Wenk MR, and Boretti FS
- Subjects
- Animals, Dogs, Female, Male, Phenotype, Time Factors, Environmental Exposure adverse effects, Glucocorticoids adverse effects, Lipidomics, Lipids blood
- Abstract
Glucocorticoids (GCs) are critical regulators of metabolic control in mammals and their aberrant function has been linked to several pathologies. GCs are widely used in human and veterinary clinical practice as potent anti-inflammatory and immune suppressive agents. Dyslipidaemia is a frequently observed consequence of GC treatment, typified by increased lipolysis, lipid mobilization, liponeogenesis, and adipogenesis. Dogs with excess GC show hyperlipidaemia, hypertension, and a higher risk of developing type 2 diabetes mellitus, but the risk of developing atherosclerotic lesions is low as compared to humans. This study aimed to examine alterations in the canine plasma lipidome in a model of experimentally induced short-term and long-term GC excess. Both treatments led to significant plasma lipidome alterations, which were more pronounced after long-term excess steroid exposure. In particular, monohexosylceramides, phosphatidylinositols, ether phosphatidylcholines, acyl phosphatidylcholines, triacylglycerols and sphingosine 1-phosphates showed significant changes. The present study highlights the hitherto unknown effects of GCs on lipid metabolism, which will be important in the further elucidation of the role and function of GCs as drugs and in metabolic and cardiovascular diseases.
- Published
- 2019
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41. MS-based lipidomics of human blood plasma: a community-initiated position paper to develop accepted guidelines.
- Author
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Burla B, Arita M, Arita M, Bendt AK, Cazenave-Gassiot A, Dennis EA, Ekroos K, Han X, Ikeda K, Liebisch G, Lin MK, Loh TP, Meikle PJ, Orešič M, Quehenberger O, Shevchenko A, Torta F, Wakelam MJO, Wheelock CE, and Wenk MR
- Subjects
- Blood Chemical Analysis standards, Blood Specimen Collection, Demography, Female, Humans, Male, Reference Standards, Blood Chemical Analysis methods, Guidelines as Topic, Lipids blood, Mass Spectrometry
- Abstract
Human blood is a self-regenerating lipid-rich biological fluid that is routinely collected in hospital settings. The inventory of lipid molecules found in blood plasma (plasma lipidome) offers insights into individual metabolism and physiology in health and disease. Disturbances in the plasma lipidome also occur in conditions that are not directly linked to lipid metabolism; therefore, plasma lipidomics based on MS is an emerging tool in an array of clinical diagnostics and disease management. However, challenges exist in the translation of such lipidomic data to clinical applications. These relate to the reproducibility, accuracy, and precision of lipid quantitation, study design, sample handling, and data sharing. This position paper emerged from a workshop that initiated a community-led process to elaborate and define a set of generally accepted guidelines for quantitative MS-based lipidomics of blood plasma or serum, with harmonization of data acquired on different instrumentation platforms across independent laboratories as an ultimate goal. We hope that other fields may benefit from and follow such a precedent., (Copyright © 2018 Burla et al. Published by The American Society for Biochemistry and Molecular Biology, Inc.)
- Published
- 2018
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42. Clathrate Hydrates of Greenhouse Gases in the Presence of Natural Amino Acids: Storage, Transportation and Separation Applications.
- Author
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Prasad PSR and Sai Kiran B
- Abstract
Storage of greenhouse gases in the form of gas hydrates is attractive and is being pursued rigorously in recent times. However, slow formation rate and inefficient water to hydrate conversion are the main hindering factors. In this report, we examine the role of two amino acids (0.5 wt%), l-methionine (l-met) and l-phenylalanine (l-phe) on the formation of gas hydrates using methane (CH
4 ), carbon dioxide (CO2 ) and their mixtures as guest molecules. Experiments are conducted under non-stirred and isochoric configurations. The hydrate conversion efficiency of both amino acids is identical for hydrates formed with CH4 and mixture of (CO2 +CH4 ). However, the hydrate conversion is significantly less in CO2 hydrates in l-phe system. Addition of amino acids to the water dramatically improved the kinetics of hydrate formation and 90% of maximum gas uptake in hydrate phase occurred in less than an hour. The water to hydrate conversion is also very efficient (>85%) in the presence of amino acids. Therefore, the amino acids containing systems are suitable for storing both CH4 and CO2 gases. The gas hydrates were characterised using powder x-ray diffraction (XRD) and Raman spectroscopic measurements. These measurements indicate the formation of sI hydrates and encasing of gas molecules as guests.- Published
- 2018
- Full Text
- View/download PDF
43. Sphingolipid Analysis in Clinical Research.
- Author
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Burla B, Muralidharan S, Wenk MR, and Torta F
- Subjects
- Blood Specimen Collection, Chromatography, Liquid, Humans, Mass Spectrometry, Research Design, Metabolomics methods, Sphingolipids blood
- Abstract
Sphingolipids are the most diverse class of lipids due to the numerous variations in their structural components. This diversity is also reflected in their extremely different functions. Sphingolipids are not only constituents of cell membranes but have also emerged as key signaling molecules involved in a variety of cellular functions, such as cell growth and differentiation, proliferation, and apoptotic cell death. Lipidomic analyses in clinical research have identified pathways and products of sphingolipid metabolism that are altered in several human pathologies. In this article, we describe how to properly design a lipidomic experiment in clinical research, how to handle plasma and serum samples for this purpose, and how to measure sphingolipids using liquid chromatography-mass spectrometry.
- Published
- 2018
- Full Text
- View/download PDF
44. The isolation and identification of new microalgal strains producing oil and carotenoid simultaneously with biofuel potential.
- Author
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Minhas AK, Hodgson P, Barrow CJ, Sashidhar B, and Adholeya A
- Subjects
- Base Sequence, Biomass, Chlorella metabolism, Fatty Acids metabolism, Lipids analysis, Lipids chemistry, Microalgae isolation & purification, Microalgae metabolism, Phylogeny, Sequence Alignment, Sequence Analysis, DNA, Biofuels, Carotenoids biosynthesis, Lipid Metabolism, Microalgae genetics
- Abstract
Taxonomy and phylogeny of twenty two microalgal isolates were examined using both universal and newly designed molecular primers. Among the isolates, Scenedesmus bijugus, Coelastrella sp., Auxenochlorella protothecoides, and Chlorella sp. were particularly promising in terms of producing lipids as measured by fatty acid methyl esters (FAME) analysis and significant concentration of carotenoids. A comparative experiment showed that S. bijugus and Chlorella sp. were the most promising candidates (L(-)(1)d(-)(1), with biomass) 174.77±6.75, 169.81±5.22mg, lipids 40.14±3.31, 39.72±3.89mg, lutein 0.47, 0.36mg, and astaxanthin 0.27, 0.18mg respectively. The fatty acids produced by these microalgal isolates were mainly palmitic, stearic, oleic, linoleic, and linolenic acid. The freshwater microalgal isolate S. bijugus be the most suitable isolate for producing biodiesel and carotenoids, due to high productivity of biomass, lipids, metabolites, and its suitable fatty acid profile., (Copyright © 2016 Elsevier Ltd. All rights reserved.)
- Published
- 2016
- Full Text
- View/download PDF
45. Wounding of Arabidopsis halleri leaves enhances cadmium accumulation that acts as a defense against herbivory.
- Author
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Plaza S, Weber J, Pajonk S, Thomas J, Talke IN, Schellenberg M, Pradervand S, Burla B, Geisler M, Martinoia E, and Krämer U
- Subjects
- Animals, Butterflies pathogenicity, Gene Expression Regulation, Plant, Herbivory, Larva pathogenicity, Arabidopsis metabolism, Arabidopsis parasitology, Cadmium metabolism, Plant Leaves metabolism, Plant Leaves parasitology
- Abstract
Approximately 0.2% of all angiosperms are classified as metal hyperaccumulators based on their extraordinarily high leaf metal contents, for example >1% zinc, >0.1% nickel or >0.01% cadmium (Cd) in dry biomass. So far, metal hyperaccumulation has been considered to be a taxon-wide, constitutively expressed trait, the extent of which depends solely on available metal concentrations in the soil. Here we show that in the facultative metallophyte Arabidopsis halleri, both insect herbivory and mechanical wounding of leaves trigger an increase specifically in leaf Cd accumulation. Moreover, the Cd concentrations accumulated in leaves can serve as an elemental defense against herbivory by larvae of the Brassicaceae specialist small white (Pieris rapae), thus allowing the plant to take advantage of this non-essential trace element and toxin. Metal homeostasis genes are overrepresented in the systemic transcriptional response of roots to the wounding of leaves in A. halleri, supporting that leaf Cd accumulation is preceded by systemic signaling events. A similar, but quantitatively less pronounced transcriptional response was observed in A. thaliana, suggesting that the systemically regulated modulation of metal homeostasis in response to leaf wounding also occurs in non-hyperaccumulator plants. This is the first report of an environmental stimulus influencing metal hyperaccumulation.
- Published
- 2015
- Full Text
- View/download PDF
46. Functions of ABC transporters in plants.
- Author
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Kretzschmar T, Burla B, Lee Y, Martinoia E, and Nagy R
- Subjects
- ATP-Binding Cassette Transporters metabolism, Subcellular Fractions metabolism, ATP-Binding Cassette Transporters physiology, Plants metabolism
- Abstract
ABC (ATP-binding cassette) proteins are ubiquitously found in prokaryotes and eukaryotes and generally serve as membrane-intrinsic primary active pumps. In higher plants, ABC proteins constitute a large family, grouped phylogenetically into eight clusters, subfamilies ABCA-ABCI (ABCH is not found in plants). ABC transporters shuttle substrates as diverse as lipids, phytohormones, carboxylates, heavy metals, chlorophyll catabolites and xenobiotic conjugates across a variety of biological membranes. To date, the largest proportions of characterized members have been localized to the plasma membrane and the tonoplast, with dominant implications in cellular secretion and vacuolar sequestration, but they are also found in mitochondrial, plastidal and peroxisomal membranes. Originally identified as tonoplast-intrinsic proteins that shuttle xenobiotic conjugates from the cytosol into the vacuole, thus being an integral part of the detoxification machinery, ABC transporters are now recognized to participate in a multitude of physiological processes that allow the plant to adapt to changing environments and cope with biotic and abiotic stresses.
- Published
- 2011
- Full Text
- View/download PDF
47. Plant ABC Transporters.
- Author
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Kang J, Park J, Choi H, Burla B, Kretzschmar T, Lee Y, and Martinoia E
- Abstract
ABC transporters constitute one of the largest protein families found in all living organisms. ABC transporters are driven by ATP hydrolysis and can act as exporters as well as importers. The plant genome encodes for more than 100 ABC transporters, largely exceeding that of other organisms. In Arabidopsis, only 22 out of 130 have been functionally analyzed. They are localized in most membranes of a plant cell such as the plasma membrane, the tonoplast, chloroplasts, mitochondria and peroxisomes and fulfill a multitude of functions. Originally identified as transporters involved in detoxification processes, they have later been shown to be required for organ growth, plant nutrition, plant development, response to abiotic stresses, pathogen resistance and the interaction of the plant with its environment. To fulfill these roles they exhibit different substrate specifies by e.g. depositing surface lipids, accumulating phytate in seeds, and transporting the phytohormones auxin and abscisic acid. The aim of this review is to give an insight into the functions of plant ABC transporters and to show their importance for plant development and survival.
- Published
- 2011
- Full Text
- View/download PDF
48. Expression analysis and functional characterization of the monosaccharide transporters, OsTMTs, involving vacuolar sugar transport in rice (Oryza sativa).
- Author
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Cho JI, Burla B, Lee DW, Ryoo N, Hong SK, Kim HB, Eom JS, Choi SB, Cho MH, Bhoo SH, Hahn TR, Neuhaus HE, Martinoia E, and Jeon JS
- Subjects
- Arabidopsis genetics, Biological Transport, Cloning, Molecular, Genetic Complementation Test, Glucose metabolism, Glucuronidase metabolism, Green Fluorescent Proteins metabolism, Molecular Sequence Data, Organ Specificity, Oryza cytology, Phylogeny, Plant Proteins genetics, Plant Proteins metabolism, Plants, Genetically Modified, Promoter Regions, Genetic genetics, Recombinant Fusion Proteins metabolism, Subcellular Fractions metabolism, Carbohydrate Metabolism, Gene Expression Regulation, Plant, Membrane Transport Proteins genetics, Membrane Transport Proteins metabolism, Oryza genetics, Vacuoles metabolism
- Abstract
In Arabidopsis, the compartmentation of sugars into vacuoles is known to be facilitated by sugar transporters. However, vacuolar sugar transporters have not been studied in detail in other plant species. To characterize the rice (Oryza sativa) tonoplast monosaccharide transporters, OsTMT1 and OsTMT2, we analysed their subcellular localization using green fluorescent protein (GFP) and expression patterns using reverse-transcription polymerase chain reaction (RT-PCR), performed histochemical beta-glucuronidase (GUS) assay and in situ hybridization analysis, and assessed sugar transport ability using isolated vacuoles. Expression of OsTMT-GFP fusion protein in rice and Arabidopsis revealed that the OsTMTs localize at the tonoplast. Analyses of OsTMT promoter-GUS transgenic rice indicated that OsTMT1 and OsTMT2 are highly expressed in bundle sheath cells, and in vascular parenchyma and companion cells in leaves, respectively. Both genes were found to be preferentially expressed in the vascular tissues of roots, the palea/lemma of spikelets, and in the main vascular tissues and nucellar projections on the dorsal side of the seed coats. Glucose uptake studies using vacuoles isolated from transgenic mutant Arabidopsis (tmt1-2-3) expressing OsTMT1 demonstrated that OsTMTs are capable of transporting glucose into vacuoles. Based on expression analysis and functional characterization, our present findings suggest that the OsTMTs play a role in vacuolar glucose storage in rice.
- Published
- 2010
- Full Text
- View/download PDF
49. Highly conserved Asp-204 and Gly-776 are important for activity of the quinoprotein glucose dehydrogenase of Escherichia coli and for mineral phosphate solubilization.
- Author
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Sashidhar B, Inampudi KK, Guruprasad L, Kondreddy A, Gopinath K, and Podile AR
- Subjects
- Amino Acid Substitution genetics, Calcium metabolism, Coenzymes metabolism, Escherichia coli Proteins genetics, Glucose Dehydrogenases genetics, Models, Molecular, Mutagenesis, Site-Directed, Protein Binding, Protein Structure, Tertiary, Sequence Homology, Amino Acid, Ubiquinone metabolism, Conserved Sequence, Escherichia coli Proteins chemistry, Escherichia coli Proteins metabolism, Glucose Dehydrogenases chemistry, Glucose Dehydrogenases metabolism, Minerals metabolism, Phosphates metabolism
- Abstract
Gram-negative bacteria membrane-bound glucose dehydrogenase (m-GDH) has pyrroloquinoline quinone [PQQ (2,7,9,-tricarboxyl-1H-pyrrolo[2,3-f]quinoline-4,5-dione)] as its prosthetic group, transferring electrons to ubiquinone (UQ) in the membrane. Based on the sequence homology of the C-terminal catalytic domain (151-796 amino acid residues) we have modeled the 3D structure of Escherichia coli GDH. The geometrical parameters of the homology model structure, validated using the Ramachandran plot, revealed 95.8% of residues in the allowed regions and 2.2% of the residues in disallowed regions. From the model, we have identified five different amino acids that are specifically involved in maintaining the PQQ in the correct configuration along with a Ca(2+) ion in the active site, and two amino acids on the surface of the protein that might be involved in UQ binding or transfer of electrons to the UQ. Site-directed mutants R201A, D204A, E217L, E217A, R266Q, R266E, E591L, E591Q, E591K, L712W, L712R, G776K, G776D and G776L lost their GDH activity, while E217Q and G776A retained their function similar to that of wild-type GDH, both in terms of specific activity and mineral phosphate solubilization. Our conclusions are consistent with those previously based on model GDH produced by a different method and using a different template X-ray structure.
- Published
- 2010
- Full Text
- View/download PDF
50. Transgenic expression of glucose dehydrogenase in Azotobacter vinelandii enhances mineral phosphate solubilization and growth of sorghum seedlings.
- Author
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Sashidhar B and Podile AR
- Subjects
- Azotobacter vinelandii genetics, Cloning, Molecular, Escherichia coli enzymology, Escherichia coli genetics, Glucose 1-Dehydrogenase genetics, Inorganic Chemicals metabolism, Promoter Regions, Genetic, Recombinant Proteins biosynthesis, Recombinant Proteins genetics, Seedlings growth & development, Seedlings microbiology, Sorghum microbiology, Azotobacter vinelandii enzymology, Gene Expression, Glucose 1-Dehydrogenase biosynthesis, Phosphates metabolism, Sorghum growth & development
- Abstract
The enzyme quinoprotein glucose dehydrogenase (GDH) catalyses the oxidation of glucose to gluconic acid by direct oxidation in the periplasmic space of several Gram-negative bacteria. Acidification of the external environment with the release of gluconic acid contributes to the solubilization of the inorganic phosphate by biofertilizer strains of the phosphate-solubilizing bacteria. Glucose dehydrogenase (gcd) gene from Escherichia coli, and Azotobacter-specific glutamine synthetase (glnA) and phosphate transport system (pts) promoters were isolated using sequence-specific primers in a PCR-based approach. Escherichia coli gcd, cloned under the control of glnA and pts promoters, was mobilized into Azotobacter vinelandii AvOP and expressed. Sorghum seeds were bacterized with the transgenic azotobacters and raised in earthen pots in green house. The transgenic azotobacters, expressing E. coli gcd, showed improved biofertilizer potential in terms of mineral phosphate solubilization and plant growth-promoting activity with a small reduction in nitrogen fixation ability., (© 2009 The Authors. Journal compilation © 2009 Society for Applied Microbiology and Blackwell Publishing Ltd.)
- Published
- 2009
- Full Text
- View/download PDF
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