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.

Organogels studied by NMR

Studies on cycloalkane‐based bisamide organogelators: A new example of stochastic chiral symmetry breaking induced by sonication

Ortuno, R. M., Pi-Boleda, B., Sans, M., Campos, M., Nolis, P., Illa, O., Estévez, J. C. and Branchadell, V. (2016), Chem. Eur. J.. Accepted Author Manuscript. doi:10.1002/chem.201604818

Enantiomerically pure C16-alkyl amides derived from cis and trans cycloalkane-1,2-dicarboxylic acids, respectively, have been synthesized and their behaviour as organogelators has been investigated. These compounds include cis/trans diastereomeric cyclobutane and cyclohexane derivatives with the aim to explore the influence of the ring size as well as the relative configuration in their hierarchical self-assembly to form gels. High resolution 1H NMR spectroscopy studies allowed the determination of the dynamics of the gelation process in [D8]-toluene and the sol-gel transition temperature. The morphology and size of the aggregates have been investigated and results have shown that, in the case of cyclobutane derivatives, the cis/trans stereochemistry is not relevant for the gelation behaviour and the properties of the soft-materials obtained, but it is remarkable for cyclohexane diamides, which are better organogelators. The four compounds produce chiral aggregates despite that two of them are meso achiral molecules. We show in this work that this fact is an example of stochastic symmetry breaking induced by sonication. The self-assembly of these molecules has been modelled providing information and support about the structure and the chirality of the aggregates.

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

 

toc_joc_rdc

10th Workshop on Magnetic Resonance Spectroscopy and Imaging (MRI/MRS) Applied to Laboratory Animals

Workshop dates: November 29th – December 2nd, 2016
Registration deadline: November 14th, 2016
Registration: REGISTRATION CLOSED  online
Capacity: Workshop limited to 4 participants (first come, first served)
Contact person: Silvia Lope-Piedrafita, PhD (silvia.lope@uab.es)

This course combines a comprehensive series of lectures on the technology of Magnetic resonance spectroscopy and imaging (MRS/MRI) with hands-on laboratory sessions to provide practical demonstrations of key concepts and procedures for preclinical studies.

Whether you are considering MRI as a research tool in your lab or just would like to learn more about MRI, this workshop addresses practical aspects of experimental MRI with laboratory animals and provide valuable hands-on experience on a 7 Tesla Bruker BioSpec spectrometer.20161001_10cursomrimrs

See the workshop brochure for more information or contact Dra. Silvia Lope via email.

Mycobacteria clumping increase their capacity to damage macrophages

frontiersmicrobiology

 

“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.

fig8

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

logo_aete_600

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.

fig4

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.

Call for applications: Predoctoral 4-year fellowship in NMR Methodology

Applications are welcome for a four-year PhD position in the field of high-resolution NMR spectroscopy at the NMR Service (SeRMN) of the Universitat Autònoma of Barcelona (UAB).

The researcher will investigate the subject “Analysis of complex mixtures by NMR spectroscopy” under the joint supervision of  Dr. Teodor Parella and Dr. Míriam Pérez-Trujillo, as part of the project “Design and Application of New Methodologies in Nuclear Magnetic Resonance” (Diseño y aplicación de nuevas metodologías en resonancia magnética nuclear, CTQ2015-64436-P, 2016-2018) awarded to Dr. Teodor Parella.

This scholarship is awarded by the Spanish Ministry of Economy and Competitiveness (MINECO), through the Predoctoral Research Fellowship Program (*) and it is co-funded by the European Social Fund (ESF).

The call for applications begins September 13th, 2016, and the deadline for submissions is September 27th, 2016 at 15:00.

All information relating to the call for applications is available at the MINECO web site and at the Database of Spanish National Funding. For details or questions about the research project, contact Dr. Teodor Parella.

(*) Convocatoria de Ayudas para contratos predoctorales para la formación de doctores 2016. Plan Estatal de Investigación Científica y Técnica y de Innovación 2013-2016. Programa Estatal de Promoción del Talento y su Empleabilidad, Subprograma Estatal de Formación.

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

Portada

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 Parella and 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

New Book Release: MORPHOLOGICAL MOUSE PHENOTYPING

“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.