Category Archives: Methods & Applications

Posts describing the use of the nmr spectroscopy (MRS) methodology, either from a practical point of view (how to perform certain experiment), or from a more theoretical perspective (description of techniques and their application).

NMR identification of monstrous mycobacterial lipids in cell wall of Mycobacterium abcessus

” Trehalose polyphleates, external cell wall lipids in Mycobacterium abcessus, are associated with the formation of clumps with cording morphology, which have been associated with virulence” by M. Llorens-Fons, M. Pérez-Trujillo, E. Julián, C. Brambilla, F. Alcaide, T. F. Byrd and M. Luquin. Frontiers in Microbiology, 2017, 8:1402. DOI:

Mycobacterium abscessus is a reemerging pathogen that causes pulmonary diseases similar to tuberculosis, which is caused by Mycobacterium tuberculosis. When grown in agar medium, M. abscessus strains generate rough (R) or smooth colonies (S). R morphotypes are more virulent than S morphotypes. In searching for the virulence factors responsible for this difference, R morphotypes have been found to form large aggregates (clumps) that, after being phagocytozed, result in macrophage death. Furthermore, the aggregates released to the extracellular space by damaged macrophages grow, forming unphagocytosable structures that resemble cords. In contrast, bacilli of the S morphotype, which do not form aggregates, do not damage macrophages after phagocytosis and do not form cords. Cording has also been related to the virulence of M. tuberculosis. A comparative study of the pattern and structure of mycolic acids was performed on R (cording) and S (non-cording) morphotypes derived from the same parent strains, and no differences were observed between morphotypes. Furthermore, cords formed by R morphotypes were disrupted with petroleum ether (PE), and the extracted lipids were analyzed by thin layer chromatography, nuclear magnetic resonance spectroscopy and mass spectrometry. Substantial amounts of trehalose polyphleates (TPP) were recovered as major lipids from PE extracts, and images obtained by transmission electron microscopy suggested that these lipids are localized to the external surfaces of cords and R bacilli. The structure of M. abscessus TPP was revealed to be similar to those previously described in Mycobacterium smegmatis. Although the exact role of TPP is unknown, our results demonstrated that TPP are not toxic by themselves and have a function in the formation of clumps and cords in M. abscessus, thus playing an important role in the pathogenesis of this species.

Removal of pharmaceuticals from hospital wastewater by Pleurotus ostreatus. Identification of pharmaceuticals metabolites by NMR

“Preliminary evaluation of Pleurotus ostreatus for the removal of selected pharmaceuticals from hospital wastewater” by L. Palli,* F. Castellet‐Rovira, M. Pérez‐Trujillo, D. Caniani, M. Sarrà‐Adroguer, R. Gori Biotechnology Progress, 2017. DOI:

The fungus Pleurotus ostreatus was investigated to assess its ability to remove diclofenac, ketoprofen, and atenolol in hospital wastewater. The degradation test was carried out in a fluidized bed bioreactor testing both the batch and the continuous mode. In batch mode, diclofenac disappeared in less than 24 h, ketoprofen was degraded up to almost 50% in 5 days while atenolol was not removed. In continuous mode, diclofenac and ketoprofen removals were about 100% and 70% respectively; atenolol degradation was negligible during the first 20 days but it increased up to 60% after a peak of laccase production and notable biomass growth. In order to identify the enzymatic system involved, further experiments were carried out in flasks. Two intermediates of diclofenac and ketoprofen were detected by nuclear magnetic resonance (NMR) spectroscopy. Moreover P. ostreatus was able to reduce chemical oxygen demand of the hospital wastewater which is an important advantage comparing to other fungi in order to develop a wastewater treatment process.


Multi-Slice MRSI Analysis of Therapy Response in Preclinical Glioblastoma

Metabolomics of Therapy Response in Preclinical Glioblastoma: A Multi-Slice MRSI-Based Volumetric Analysis for Noninvasive Assessment of Temozolomide Treatment” by N. Arias-Ramos, L. Ferrer-Font,  S. Lope-Piedrafita,  V. Mocioiu, M. Julià-Sapé , M. Pumarola, C. Arús  and A. P. Candiota. Metabolites, 2017, 18;7(2). pii: E20. DOI: 10.3390/metabo7020020.

Glioblastoma (GBM) is the most common and aggressive glial primary tumor with a survival average of 14-15 months, even after application of standard treatment. Non-invasive surrogate biomarkers of therapy response may be relevant for improving patient survival. Nosological images of therapy response using a semi-supervised source extraction approach in preclinical GBM based on single slice Magnetic Resonance Spectroscopic Imaging (MRSI) was previously describe by our group. However, because of GBM heterogeneity, relevant response information could be missed just by studying one slice. Therefore, the goal of this work was to acquire 3D-like information from preclinical GBM under a longitudinal treatment protocol, using a multi-slice MRSI approach.

Nosological maps were obtained based on semi-supervised convex Non-negative Matrix Factorization and each voxel was colored according to the contribution to the spectral pattern of each one of the three sources or characteristic spectral patterns: Normal brain, actively proliferating tumour or responding tumour.

Heterogeneous response levels were observed and three arbitrary groups of treated animals were defined as: high response, intermediate response, and low response. Histopathological studies showed an inverse correlation between the responding pattern level and Ki67 proliferation rate.


Long-term fertilization determines different metabolomic profiles and responses in saplings of three rainforest tree species with different adult canopy position

Long-term fertilization determines different metabolomic profiles and responses in saplings of three rainforest tree species with different adult canopy position” by  A. Gargallo-Garriga, S. J. Wright, J. Sardans, M. Pérez-Trujillo, M. Oravec, K. Večeřová,O. Urban, M. Fernández-Martínez, T. Parella, J. Peñuelas.

Plos One, 2017, 1-21. DOI: 10.1371/journal.pone.0177030

Tropical rainforests are frequently limited by soil nutrient availability. However, the response of the metabolic phenotypic plasticity of trees to an increase of soil nutrient availabilities is poorly understood. We expected that increases in the ability of a nutrient that limits some plant processes should be detected by corresponding changes in plant metabolome profile related to such processes. We studied the foliar metabolome of saplings of three abundant tree species in a 15 year field NPK fertilization experiment in a Panamanian rainforest. The largest differences were among species and explained 75% of overall metabolome variation.

Chiral Recognition by Dissolution DNP NMR Spectroscopy of 13C-Labeled DL-Methionine

“Chiral Recognition by Dissolution DNP NMR Spectroscopy of 13C-Labeled DL-Methionine” By Eva Monteagudo, Albert Virgili, Teodor Parella and Míriam Pérez-Trujillo.Anal. Chem., 2017, 89 (9), pp 4939–4944 DOI: 10.1021/acs.analchem.7b00156

A method based on d-DNP NMR spectroscopy to study chiral recognition is described for the first time. The enantiodifferentiation of a racemic metabolite in a millimolar aqueous solution using a chiral solvating agent was performed. Hyperpolarized 13C-labeled DL-methionine enantiomers were differently observed with a single-scan 13C NMR experiment, while the chiral auxiliary at thermal equilibrium remained unobserved. The method developed entails a step forward in the chiral recognition of small molecules by NMR spectroscopy, opening new possibilities in situations where the sensitivity is limited, for example, when a low concentration of analyte is available or when the measurement of an insensitive nucleus, like 13C, is required. The advantages and current limitations of the method, as well as future perspectives, are discussed.

Mycobacteria clumping increase their capacity to damage macrophages



“Mycobacteria clumping increase their capacity to damage macrophages” by C. Brambilla, M. Llorens-Fons, E. Julián, E. Noguera-Ortega, C. Tomàs-Martínez, M. Pérez-Trujillo, T. F. Byrd, F. Alcaide and M. Luquin.

Front. Microbiol. 7:1562.  DOI: 10.3389/fmicb.2016.01562

The rough morphotypes of non-tuberculous mycobacteria have been associated with the most severe illnesses in humans. This idea is consistent with the fact that Mycobacterium tuberculosis presents a stable rough morphotype. Unlike smooth morphotypes, the bacilli of rough morphotypes grow close together, leaving no spaces among them and forming large aggregates (clumps). Currently, the initial interaction of macrophages with clumps remains unclear. Thus, we infected J774 macrophages with bacterial suspensions of rough morphotypes of Mycobacterium abscessus containing clumps and suspensions of smooth morphotypes, primarily containing isolated bacilli. Using confocal laser scanning microscopy and electron microscopy, we observed clumps of at least 5 rough-morphotype bacilli inside the phagocytic vesicles of macrophages at 3 hours post-infection. These clumps grew within the phagocytic vesicles, killing 100% of the macrophages at 72 hours post-infection, whereas the proliferation of macrophages infected with smooth morphotypes remained unaltered at 96 hours post-infection. Thus, macrophages phagocytose large clumps, exceeding the bactericidal capacities of these cells. Furthermore, proinflammatory cytokines and granuloma-like structures were only produced by macrophages infected with rough morphotypes. Thus, the present study provides a foundation for further studies that consider mycobacterial clumps as virulence factors.


Figure. Content of GPL and structure of mycolic acids. (A) 1-D TLC analysis of the crude lipid extracts of M. abscessus strains. (B) 1H-NMR spectra of purified mycolic acid methyl esters from M. abscessus. (C) Relative molar ratios of molecular moieties cis-db, trans-db, cis-cp and trans-cp of mycolic acid methyl esters from M. abscessus.

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


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.


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.


“MORPHOLOGICAL MOUSE PHENOTYPING: Anatomy, Histology and Imaging” by Jesús Ruberte París, Ana Carretero Romay, and Marc Navarro Beltrán (2016). Editorial Médica Panamericana.

Morphologial Mouse Phenotypiong_BOOKAn extraordinary atlas of mouse anatomy which includes more than 2,200 original images over 600 pages to show the anatomy, histology and cellular structure of mouse organs. This book attempts to provide an overview of the different levels of morphology of the mouse, ranging from gross anatomy and topographical anatomy (to explain the relative position of the organs and structures of a particular body region) down to the microscopic anatomy. Imaging technologies used for that include magnetic resonance imaging (MRI), computed tomography (CT), ultrasonography, angiography, X-ray, and electron microscopy. Also, classical anatomical techniques such as conventional dissection, skeletal preparations, vascular injections, histology and immunohistochemistry have been employed to characterize the mouse morphology.

All MRI images included in this book were acquired at our NMR facility (SeRMN, Universitat Autònoma de Barcelona) in a 7 Tesla Bruker BioSpec spectrometer.

André Fredi’s oral presentation at 8th GERMN / 5th Iberian NMR Meeting

André Fredi made an oral presentation at the 8th GERMN / 5th Iberian NMR Meeting (GERMN 2016) held in Valencia, Spain from 27th to 29th June 2016.

In his presentation, that was titled  Exploring the use of Generalized Indirect Covariance to reconstruct Pure Shift NMR spectra: Current Pros and Cons”, André explained how to make pure spectra shift from Generalized Indirect IMG-20160628-WA0028Covariance processing (psGIC). This new method is basically a new way to get “synthetic” pure shift spectra without the need to purchase a pure shift spectrum in the spectrometer and without the penalties that pure-shift experiments cause.

André has been working as a Ph.D. candidate at the Department of Chemistry and SeRMN under the direction of Dr. Teodor Parella and Dr. Pau Nolis since November 2014, when he enrolled in the Department of Chemistry doctoral program at Universitat Autònoma de Barcelona with a fellowship from CNPq-Brazil. He is currently in his second year and expects to defend the doctoral thesis on 2017/2018.


Presentations at the EUROMAR 2016 Conference


André Fredi (PhD student) and Teodor Parella presented our last research works at the annual meeting of the European magnetic resonance community EUROMAR 2016 Conference that was celebrated on days 3th to 7th July in Aarhus, Denmark. Find below a summary of our contributions. Continue reading Presentations at the EUROMAR 2016 Conference