Tag Archives: metabolomics

SeRMN contribution to the 32nd AETE (European Embryo Transfer Association) Meeting

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The 32nd European Embryo Transfer Association Meeting of 2016 was held in Barcelona (from the 9th to the 10th of September).

We presentented the poster:

Nuclear magnetic resonance (NMR) of goat follicular fluid shows different metabolic profiles among follicle size and female age” of S. Soto, M. Pérez-Trujillo, M.G. Catalá, M. Roura, D. Izquierdo, T. Parella, M.T. Paramio.

Abstract: Oocytes recovered from prepubertal goats are very heterogeneous in growth and grade of atresia which make them unpredictable for IVEP programs. We have observed that oocytes from prepubertal goats obtained from >3 mm follicles develop up to blastocyst stage at a similar percentage than oocytes from adult goats (18% vs 21%), suggesting that the follicle development and the follicular fluid (FF) content are more relevant to oocyte competence than the age of the donor. The aim of this study is to characterize the FF metabolomic profile from different follicular environments through a high-resolution 1H NMR-based metabolomic study. Samples of adult (n=40) and prepubertal (n=16) FF where collected by laparoscopic ovum pick-up (LOPU) and by aspiration of slaughterhouse ovaries, respectively. FF from small (< 3 mm) and large (> 3 mm) diameter follicles where pooled for each female. Multivariate ordination principal component analysis (PCA) was performed to detect patterns of sample ordination in the metabolomes. The unsupervised method clearly differed between the FF metabolomes of large and small follicles of prepubers and between the FF of preadolescent and adult individuals.

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Figure. a) PCA scores plot (PC1-PC2) from 1H NMR spectral data of follicular fluid samples of preadolescent (n=16; blue dots) and adult (n=40; black dots) goats. b) PCA heat map loadings plot (PC1-PC2) with some discriminant variables assigned.

PhD Thesis by Albert Gargallo Garriga: Publications and Data Sets

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The links below point to the research articles and Mass Spectrometry and NMR Spectroscopy raw datasets that were part of my thesis work. The last link points to my Ph.D. Thesis in pdf format.

Chapter 1

MEE“Ecometabolomics: Optimized NMR-based method” by Albert Rivas-Ubach, Miriam Pérez-Trujillo, Jordi Sardans, Albert Gargallo-Garriga, Teodor Parella, Josep Peñuelas. Methods in Ecology and Evolution, February 2013. DOI: 10.1111/2041-210X.12028

Chapter 4

scireportsOpposite metabolic responses of shoots and roots to drought by Albert Gargallo-Garriga, Jordi Sardans, Míriam Pérez-Trujillo, Albert Rivas-Ubach, Michal Oravec, Teodor Parella and Josep Peñuelas. Scientific reports 4, Article number: 6829, October 2014. DOI: 10.1038/srep06829

Chapter 5

Warming differentially influences the effects of drought on stoichiometry and metabolomics in shoots and roots” by Albert Gargallo-Garriga, Jordi Sardans, Míriam Pérez-Trujillo, Michal Oravec,Otmar Urban, Anke Jentsch, Juergen Kreyling, Carl Beierkuhnlein Teodor Parellaand Josep Peñuelas. New Phytologist. March 2015. DOI: 10.1111/nph.13377

Chapter 6

Plant Biology“Metabolomic responses of Quercus ilex seedlings to wounding simulating herbivory” By Jordi Sardans, Albert Gargallo-Garriga,Míriam Pérez-Trujillo, Teodor Parella, Roger Seco, Iolanda Filella, Josep  Peñuelas. Plant biology. April 2013. DOI: 10.1111/plb.12032

Chapter 7

Ph.D. Thesis

Shifts in plant foliar and floral metabolomes in response to the suppression of the associated microbiota

logo_BMCPB“Shifts in plant foliar and floral metabolomes in response to the suppression of the associated microbiota” by A. Gargallo-Garriga, J. Sardans, M. Pérez-Trujillo, A. Guenther, J. Llusià, L. Rico, J. Terradas, G. Farré-Armengol, I. Filella, T. Parella and J. Peñuelas. BMC Plant Biology 2016; 16:78. DOI: 10.1186/s12870-016-0767-7

The significance of microbial populations to the health and physiology of human and animal hosts has become a burgeoning and increasingly newsworthy topic. Of course, plants are also hosts for microbial life, and our metabolomics new study in BMC Plant Biology suggests that microbial influence on plant biology is more complex than we currently appreciate. Continue reading Shifts in plant foliar and floral metabolomes in response to the suppression of the associated microbiota

Visiting PhD Student Yaoyao Wang

Blog2Today we are saying goodbye to our dear Yaoyao, though we hope to see her very soon again.

Yaoyao is currently finishing her PhD on metabonomics applied to clinical biomarkers in the Legido-Quigley Lab at King’s College London (KCL).

She has been visiting us for the last two months, during which we have been working together in two metabonomics projects related to drug misuse biomarkers and chiral metabonomics. It has been a great pleasure for us to spend this time with her and continue with this collaboration from now on.

Seminar: Biomarker and metabolomics, a novel approach to detect drug misuse

Yaoyao Wang, visiting PhD student from King’s College London, will be giving a talk on  December the 18th at 10:00 h in the SeRMN. Her talk is entitled “Biomarker and metabolomics: a novel approach to detect drug misuse”.

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Yaoyao is from Clinical Biomarkers Lab of the Institute of Pharmaceutical Science, King’s College London (KCL). Her PhD project focuses on developing metabolomics approach to identify biomarkers for drug misuse through the analysis of human biofluids samples and the development of data treatment methods, using R (XCMS) and other bioinformatics tools. She has been collaborating intensively with the Drug Control Centre of KCL using LC-MS.

Her talk will include the metabolomics biomarker discovery of low dose salbutamol in urine collected for anti-doping tests and preliminary longitudinal metabolomics study of “date-rape” drug GHB, as well as a glance of the other on-going projects in Clinical Biomarkers Lab.

All interested people are welcome to attend this seminar.

PhD Thesis Defense: Metabolomics and stoichiometry adapted to the study of environmental impacts on plants. PhD Thesis by Albert Gargallo Garriga

 

I am defending my PhD thesis next Thursday (September 10, 2015) at 11.30am in the Sala d´Actes “Carles Miravitlles” of the Institut de Ciències de Materials de Barcelona (ICMAB), Campus UAB. The title of my thesis is “Metabolomics and stoichiometry adapted to the study of environmental impacts on plants” and below you can find an abstract of the work. If you are interested you are very welcome.

 

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Metabolomics has allowed significant advances in biological sciences. An increasing number of ecological studies have applied a metabolomic approach to answer ecological questions (ecometabolomics) during the last few years. The work developed throughout this PhD thesis means a further step in the field of ecometabolomics. Continue reading PhD Thesis Defense: Metabolomics and stoichiometry adapted to the study of environmental impacts on plants. PhD Thesis by Albert Gargallo Garriga

Warming differentially influences the effects of drought on stoichiometry and metabolomics in shoots and roots

“Warming differentially influences the effects of drought on stoichiometry and metabolomics in shoots and roots” by Albert Gargallo-Garriga, Jordi Sardans, Míriam Pérez-Trujillo, Michal Oravec,Otmar Urban, Anke Jentsch, Juergen Kreyling, Carl Beierkuhnlein Teodor Parella and Josep Peñuelas. New Phytologist. March 2015. DOI: 10.1111/nph.13377

Plants in natural environments are increasingly being subjected to a combination of abiotic stresses, such as drought and warming, in many regions. The effects of each stress and the combination of stresses on the functioning of shoots and roots have been studied extensively, but little is known about the simultaneous metabolome responses of the different organs of the plant to different stresses acting at once. We studied the shift in metabolism and elemental composition of shoots and roots of two perennial grasses, Holcus lanatus and Alopecurus pratensis, in response to simultaneous drought and warming. Continue reading Warming differentially influences the effects of drought on stoichiometry and metabolomics in shoots and roots

In vivo MRS and ex vivo HRMAS in an Ischemic Rat Stroke Model

JCBMcover“In vivo and ex vivo Magnetic Resonance Spectroscopy of the Infarct and the Subventricular Zone in Experimental Stroke” by E. Jiménez-Xarrié, M. Davila, S. Gil-Perotín, A. Jurado-Rodríguez, A.P. Candiota, R. Delgado-Mederos, S. Lope-Piedrafita, J.M. García-Verdugo, C. Arús, J. Martí-Fàbregas. Journal of Cerebral Blood Flow & Metabolism, 2015, 35:828–834. DOI: 10.1038/jcbfm.2014.257

Ischemic stroke changes the metabolic pattern in the infarct area and also in other regions such as the ipsilateral subventricular zone (SVZi) where neural progenitor cells (NPCs) proliferation is enhanced in the mammalian and human brains. Magnetic resonance spectroscopy (MRS) provides metabolic information in vivo. With regard to NPCs proliferation, a resonance at 1.28 ppm has been described as an in vivo MRS biomarker of NPCs in the hippocampus of rats and humans. Continue reading In vivo MRS and ex vivo HRMAS in an Ischemic Rat Stroke Model

Hyperpolarized 13C Magnetic Resonance in Acute Liver Failure Rats

2014_coverNMinBiomedReal-time assessment of 13C metabolism  reveals an early lactate increase in the brain of rats with acute liver failure” by Laia Chavarria, Jordi Romero-Giménez, Eva Monteagudo, Silvia Lope-Piedrafita, Juan Cordoba. NMR in Biomedicine (2014) 28:17-23. DOI: 10.1002/nbm.3226

Intracranial hypertension is a severe complication of acute liver failure (ALF) secondary to brain edema. The pathogenesis of cerebral edema in ALF is not clear, but seems to be related to energy metabolism in which lactate may have an important role. The aim of this study was to follow the synthesis of brain lactate using a novel in vivo metabolic technology in a rat model of ALF. Continue reading Hyperpolarized 13C Magnetic Resonance in Acute Liver Failure Rats

Opposite metabolic responses of shoots and roots to drought

scireports Opposite metabolic responses of shoots and roots to drought by Albert Gargallo-Garriga, Jordi Sardans, Míriam Pérez-Trujillo, Albert Rivas-Ubach, Michal Oravec, Teodor Parella and Josep Peñuelas. Scientific reports 4, Article number: 6829, October 2014. DOI: 10.1038/srep06829

Shoots and roots are autotrophic and heterotrophic organs of plants with different physiological functions. Do they have different metabolomes? Do their metabolisms respond differently to environmental changes such as drought? We used metabolomics and elemental analyses to answer these questions. Continue reading Opposite metabolic responses of shoots and roots to drought