Category Archives: Our Research

These are short reports about the research activities carried out at the SeRMN.
In them we describe the work done in collaboration with research groups, to summarize communications presented at scientific meetings, to report visits and stages at other laboratories or facilities, and to comment the meetings and workshops we have attended.

Solving JHH measurement in overcrowded regions

Accurate measurement of JHH in overlapped signals by a TOCSY-edited SERF Experiment

André Fredi, Pau Nolis* and Teodor Parella*

Magnetic Resonance in ChemistryDOI: 10.1002/mrc.4572

Selective Refocusing (GSERF or the recent PSYCHEDELIC) experiments were originally designed to determine all proton-proton coupling constants (JHH) for a selected proton resonance. They work for isolated signals on which selective excitation can be successfully applied but, as happens in other selective experiments, fail for overlapped signals. To circumvent this limitation, a doubly-selective TOCSY-GSERF scheme is presented for the measurement of JHH in protons resonating in crowded regions. This new experiment takes advantage of the editing features of an initial TOCSY transfer to uncover hidden resonances that become accessible to perform the subsequent frequency-selective refocusing.

RDC measurements and application

joceah_v081i019.inddApplication to the structural discrimination of small molecules containing multiple stereocenters. One-Shot determination of residual dipolar couplings.
Castañar, L.; Garcia, M.; Hellemann, E.; Nolis, P.; Gil, R.; Parella, T.


A novel approach for the fast and efficient structural discrimination of molecules containing multiple stereochemical centers is described. A robust Jresolved HSQC experiment affording highly resolved 1JCH/1TCHsplittings along the indirect dimension and homodecoupled 1H signals in the detected dimension is proposed. The experiment enables in-situ distinction of both isotropic and anisotropic components of molecules dissolved incompressed PMMA gels, allowing a rapid and direct one-shot determination of accurate residual dipolar coupling constants from a single NMR spectrum



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.

SeRMN at the SMASH NMR 2016 Conference

Some of our last research works has been presented at the annual meeting of the SmallMolecule NMR Conference (SMASH) that has been taken place in La Jolla (USA) from 11thto 14thSeptember 2016.

Teodor Parella presented two posters.
“In situ determination of 1DCH and 2DHH RDCs from a single 1JCH/2JHH -resolved NMR measurement” of Núria Marcó García, Roberto R. Gil and Teodor Parella.

Abstract: A fast RDC-assisted strategy involving the simultaneous determination of isotropic (scalar) and anisotropic (total) interactions is reported. The concerted use of individual 1DCH for all CHn multiplicities and 2DHH obtained from a single 1JCH/2JHH-resolved NMR spectrum offers an unambiguous assignment of diastereotopic protons and an efficient discrimination between all eight possible diastereoisomeric structures of strychnine which contains six stereocenters.

Figure: 500.13MHz JCH/JHH-Resolved spectra of 1 in A) isotropic CDCl3 and B) anisotropic PMMA-CDCl3 (2H nQ(CDCl3)=26 Hz) conditions. The projections along the F2 dimension are the conventional 1H spectrum in isotropic conditions and the 1H-CPMG spectrum in anisotropic conditions, respectively.

“Pure shift NMR covariance” of André Fredi, Pau Nolis, Carlos Cobas, Gary E. Martin, Teodor Parella.

Abstract: The development of novel experimental strategies to significantly enhance signal resolution by broadband homodecoupling is a current topic of high interest in 1H NMR spectroscopy . A number of different building blocks have been implemented into 1D and 2D homo- and heteronuclear experiments in order to provide resolution-enhanced pure chemical shift 1H NMR spectra, where signals appear collapsed to singlets. On the other hand, Covariance processing methods have been used to generate challenging NMR spectral representations . We present here the first attempts towards a general solution to generate Pure Shift NMR spectra by using Generalized Indirect Covariance (psGIC) co-processing3,4 . The current strategy is based on the calculation of a new 2D psGIC spectrum from the combination of a parent homo- or heteronuclear spectrum and a reference 2D F1-homodecoupled 1H- 1H correlation spectrum only showing diagonal cross-peaks (DIAG), which share a common 1H frequency dimension. Using psGIC, the F1 dimension in the DIAG spectrum is transferred to the F2 dimension of the parent spectrum, thus generating a new pure shift 2D spectrum

Figure: Generation of Pure Shift NMR spectra by using Generalized Indirect Covariance (psGIC)

PhD Thesis by Albert Gargallo Garriga: Publications and Data Sets


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

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

Chloroperoxidase-catalyzed amino alcohol oxidation: Substrate specificity and novel strategy for the synthesis of N-Cbz-3-aminopropanal

S00329592“Chloroperoxidase-catalyzed amino alcohol oxidation: Substrate specificity and novel strategy for the synthesis of N-Cbz-3-aminopropanal” by G. Masdeu,  M. Pérez-Trujillo, J. López-Santín and Gregorio Álvaro. Process Biochemistry 2016; DOI:10.1016/j.procbio.2016.05.022

The ability of chloroperoxidase (CPO) to catalyze amino alcohol oxidations was investigated. The oxidations of compounds with different configurations with respect to the amine position towards hydroxyl – using H2O2 and tert-butyl hydroperoxide (t-BuOOH) – were analyzed in terms of the initial reaction rate, substrate conversion, and CPO operational stability. Continue reading Chloroperoxidase-catalyzed amino alcohol oxidation: Substrate specificity and novel strategy for the synthesis of N-Cbz-3-aminopropanal

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