13th Workshop on Magnetic Resonance Spectroscopy and Imaging (MRI/MRS) Applied to Laboratory Animals

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Workshop dates:May 24th – 27th, 2022
Registration deadline:May 13th, 2022
Registration:download the registration form and email it to
Capacity:Workshop limited to 4 participants (first come, first served)
Contact person:Silvia Lope-Piedrafita, PhD ()

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.

See the workshop brochure for more information, or contact via email.

PhD Thesis: Advances in NMR spectroscopic methodology and applications: time-efficient methods, ultra long-range heteronuclear correlation experiments and enantiospecific analysis of complex mixtures.

Methods & Applications, News from the SeRMN, Our Research

Last 21st October 2021 I defended my PhD Thesis entitled: Advances in NMR spectroscopic methodology and applications: time-efficient methods, ultra long-range heteronuclear correlation experiments and enantiospecific analysis of complex mixtures.

The thesis is divided into the following topics:

  • the development of Nuclear Magnetic Resonance (NMR) experiments focused on efficiency in terms of time;
  • establishing new pulse sequences that facilitate the study of long-distance coupling constants fundamental for structural elucidation;
  • the development of a reliable method that allows the differentiated analysis of enantiomers (enantiospecific) directly from its original mixture (in situ) and from multiple molecules simultaneously (multicomponent).

The NMR experiments developed using the MFA (Multiple Fid Acquisition) approach based on the “afterglow magnetization”, allows a considerable reduction of the experimental time by acquiring several experiments at the same time, which are stored in different FIDs that can be visualized separately. In this thesis several works are presented that allow to make a structural elucidation of organic molecules in a fast, simple and unambiguous way, among them MFA-COSY / RELAY3, MFA-COSY / TOCSY, MFA-HMBC / HMBC-COSY, MFA-MBOB -COSY, MFA-TOCSY / TOCSY, MFA-HSQC / HSQC and the MFA-HSQC / Pure-shiftHSQC. Furthermore, with an adequate combination of MFA and “Spectral Aliasing” (SA), a new experiment is presented, which in addition to the experimental time improves spectral resolution and facilitates structural identification. The SA, despite being a powerful experiment to avoid signal overlapping has an important disadvantage related to the identification of each signal, to avoid this problem, for a few extra seconds, we acquired the two heteronuclear experiments in 2D, the HSQC with “Spectral Aliasing” and the standard HSQC to facilitate signal assignment.

Furthermore, in terms of improving the spectral resolution, this thesis presents two experiments following the Pure-shift methodology to eliminate the proton-proton coupling constant, using BIRD (BIlinear Rotation Decoupling) to perform heteronuclear decoupling, minimizing signal overlapping. The novelty of this work is based on the detection of multiple nuclei in the same 2D spectrum, nitrogen and carbon in the indirect dimension (F1) and proton in F2, is what is known as “Time-Shared NMR experiments”. In addition, using the same approach, a second experiment is presented that allows the calculation (via direct observation) of the heteronuclear proton-carbon and proton-nitrogen coupling constants simultaneously. The measurement of long-distance heteronuclear coupling constants remains a challenge in NMR spectroscopy, due to their tiny values and to the difficulty of their measurement. A modification in the LR-HSQMBC (changing some 180º pulses of the experiment by selective pulses irradiated in an area of the spectrum) allows the measurement of very small coupling constants (of up to 6 separation bonds). In this work, the advantages of the new LR-selHSQMBC NMR experiment are exposed and the advantages and disadvantages of both experiments are compared.

Finally, this thesis presents an innovative work related to the enantiospecific and simultaneous detection of multiple pairs of enantiomers in a mixture without prior separation or derivatization of the sample components and with minimal sample manipulation. This method is based on NMR spectroscopy and on the use of a chiral solvating agent (CSA) as chiral auxiliary. This work shows, as a proof of concept, the simultaneous enantiospecific detection of multiple enantiomeric pairs directly within the original mixture. This is demonstrated with an aqueous mixture of the essential amino acids in their D and L forms.

The thesis can be downloaded in PDF format from the TDX repository and from the TESEO repository.

ACKNOWLEDGMENTS

I would like to thank the financial support for this research by Spanish MINECO projects “Diseño y Aplicación de Nuevas Metodologías en Resonancia Magnética Nuclear” (CTQ2015-64436-P) and “Metodologías Modernas en Resonancia Magnética Nuclear de Moleculas Pequeñas” (PGC2018-095808-B-I00) and for the grant BES-2016-078903 awarded by Agencia Estatal de Investigación.

SeRMN contribution to SMASH Small Molecule NMR Conference

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Kumar Motiram-Corral is presenting at SMASH 2021 Conference a talk entitled In situ Enantiospecific Detection of Multiple Metabolites in Mixtures using NMR Spectroscopy, related to some of our recent research work. The presentation will be 1st of September in the section “Unveiling the Unknown – New Methods in Structure Elucidation“.

L. T. Kuhn, K. Motiram-Corral, T. J. Athersuch, T. Parella, M. Pérez-Trujillo, Angew. Chem. Int. Ed. 59 (2020) 23615.

Metabolomics and transcriptomics to decipher molecular mechanisms underlying ectomycorrhizal root colonization of an oak tree

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M. Sebastiana, A. Gargallo-Garriga, J. Sardans, M. Pérez-Trujillo, F. Monteiro, A. Figueiredo, M. Maia, R. Nascimento, M. Sousa Silva, A. N. Ferreira, C. Cordeiro, A. P. Marques, L. Sousa, R. Malhó & J. Peñuelas

Scientific Reports volume 11, Article number: 8576 (2021). https://doi.org/10.1038/s41598-021-87886-5

Mycorrhizas are known to have a positive impact on plant growth and ability to resist major biotic and abiotic stresses. However, the metabolic alterations underlying mycorrhizal symbiosis are still understudied. By using metabolomics and transcriptomics approaches, cork oak roots colonized by the ectomycorrhizal fungus Pisolithus tinctorius were compared with non-colonized roots. Results from this global metabolomics analysis suggest decreases in root metabolites which are common components of exudates, and in compounds related to root external protective layers which could facilitate plant-fungal contact and enhance symbiosis. Root metabolic pathways involved in defense against stress were induced in ectomycorrhizal roots that could be involved in a plant mechanism to avoid uncontrolled growth of the fungal symbiont in the root apoplast. Several of the identified symbiosis-specific metabolites, such as GABA, may help to understand how ectomycorrhizal fungi such as P. tinctorius benefit their host plants.

SeRMN contribution at EUROMAR 2021 Conference

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Some of our recent research work was presented at the European NMR meeting Euromar 2021 that was going to take place at Portoroz (Slovenia), but which was finally virtual from the 5th to the 8th of July 2021.

· Míriam Pérez-Trujillo presented the talk In situ Enantiospecific Detection of Multiple Metabolites in Mixtures using NMR Spectroscopy in the “Metabolomics” session. In this talk our last advances in enantiodifferentiation using NMR were shown and discussed.

To date, the enantiospecific analysis of mixtures necessarily requires prior separation of the individual components. The simultaneous enantiospecific detection of multiple chiral molecules in a mixture represents a major challenge, which would lead to a significantly better understanding of the underlying biological processes; e.g. via enantiospecifically analyzing metabolites in their native environment. Here, we report on the first in situ enantiospecific detection of a thirty-nine-component mixture. As a proof of concept, eighteen essential amino acids (AAs) at physiological concentrations were simultaneously enantiospecifically detected using NMR spectroscopy and a chiral solvating agent. This work represents a first step towards the simultaneous multicomponent enantiospecific analysis of complex mixtures, a capability that will have substantial impact on metabolism studies, metabolic phenotyping, chemical reaction monitoring, and many other fields where complex mixtures containing chiral molecules require efficient characterization.

L. T. Kuhn, K. Motiram-Corral, T. J. Athersuch, T. Parella, M. Pérez-Trujillo, Angew. Chem. Int. Ed. 59 (2020) 23615.

Yeast Pichia pastoris for bulk chemicals production

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Benchmarking recombinant Pichiapastoris for 3-hydroxypropionic acid production from glycerol

A. Fina, G. Coelho Brêda, M. Pérez-Trujillo, D. M. Guimarães Freire, R. Volcan Almeida, J. Albiol, P. Ferrer

Microb. Biotechnol. (2021) 14(4), 1671– 1682. https://doi.org/10.1111/1751-7915.13833

The use of the methylotrophic yeast Pichia pastoris (Komagataella phaffi) to produce heterologous proteins has been largely reported. However, investigations addressing the potential of this yeast to produce bulk chemicals are still scarce. In this study, we have studied the use of P. pastoris as a cell factory to produce the commodity chemical 3-hydroxypropionic acid (3-HP) from glycerol. 3-HP is a chemical platform which can be converted into acrylic acid and to other alternatives to petroleum-based products. To this end, the mcr gene from Chloroflexus aurantiacus was introduced into P. pastoris. This single modification allowed the production of 3-HP from glycerol through the malonyl-CoA pathway. Found results benchmark P. pastoris as a promising platform to produce bulk chemicals for the revalorization of crude glycerol and, in particular, to produce 3-HP.

SeRMN contributions at 10th GERMN biennial /9th IberAmerican/7th Iberian NMR Meeting

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Some of the SeRMN staff has presented our recent research work at the biannual Spanish and IberAmerican NMR meeting, 10th GERMN biennial /9th IberAmerican/7th Iberian NMR Meeting. This year it was a virtual meeting taking place from 26 to 29 April 2021.

Pau Nolis presented an oral communication entitled “Reducing experimental time using Multiple Fid Acquisition“. P. Nolis, K. Motiram-Corral, M. Pérez-Trujillo, T. Parella.

Speeding-up NMR molecular analysis is an important research field which has been continuously advancing since NMR early days. The relevant benefits are clear and evident: i) reduce analysis time per sample => reduce analysis cost; ii) gain spectrometer time to analyze new samples => improve spectrometer efficiency. Multiple FID Acquisition (MFA) strategy consists in the design of NMR pulse sequence experiments accommodating N acquisition windows, each registering different relevant structural information. This strategy is faster
than perform a traditional sequential acquisition of N separated experiments. Several design strategies and practical experiments will be shown and discussed.

Míriam Pérez-Trujillo presented an oral communication entitled “Simultaneous Enantiospecific Detection of Multiple Metabolites in Mixtures using NMR Spectroscopy“. L. T. Kuhn, K. Motiram-Corral, T. J. Athersuch, T. Parella, M. Pérez-Trujillo.

Chirality plays a fundamental role in nature, but its detection and quantification still face many limitations. To date, the enantiospecific analysis of mixtures necessarily requires prior separation of the individual components. The simultaneous enantiospecific detection of multiple chiral molecules in a mixture represents a major challenge, which would lead to a
significantly better understanding of the underlying biological processes; e.g. via enantiospecifically analyzing metabolites in their native environment. Here, we report on the first in situ enantiospecific detection of a thirty-ninecomponent mixture. As a proof of concept, eighteen essential amino acids (AAs) at physiological concentrations were simultaneously enantiospecifically detected using NMR spectroscopy and a chiral solvating agent. This work
represents a first step towards the simultaneous multicomponent enantiospecific analysis of complex mixtures, a capability that will have substantial impact on metabolism studies, metabolic phenotyping, chemical reaction monitoring, and many other fields where complex mixtures containing chiral molecules require efficient characterization.

Special Issue: NMR-Based Metabolomics

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Special Issue: NMR-Based Metabolomics, by Míriam Pérez-Trujillo* and Toby J. Athersuch*

Molecules2021, 26(11), 3283; https://doi.org/10.3390/molecules26113283

This article belongs to the Special Issue NMR-Based Metabolomics

Nuclear magnetic resonance (NMR) spectroscopy remains one of the core analytical platforms for metabolomics, providing complementary chemical information to others, such as mass spectrometry, and offering particular advantages in some areas of research on account of its inherent robustness, reproducibility, and phenomenal dynamic range. While routine experimental protocols for profiling and related statistical analysis pipelines have been established, they often present considerable challenges to the analyst, including spectral overlap, accurate and precise quantification, and chemical shift variation. Consequently, there is still much activity across all areas of NMR spectroscopic analysis in relation to metabolomics. Furthermore, there remain many biological systems and sample types that have not been extensively explored using NMR spectroscopy-based metabolomics.In this Special Issue, several advances in methodology, and new applications in the field of NMR-based metabolomics, have been presented. In addition, the SI includes authoritative review articles focused on the state-of-the-art of quantitative NMR spectroscopy in biomedical metabolomics applications, and novel applications in the agri-food sector.

Metabolomic fingerprinting of pig seminal plasma identifies in vivo fertility biomarkers

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PREPRINT VERSION AT Journal of Animal Science and Biotechnology

Yentel Mateo-Otero, Pol Fernández-López, Ariadna Delgado-Bermúdez, Pau Nolis, Jordi Roca, Jordi Miró, Isabel Barranco, Marc Yeste

Background

Metabolomic approaches, which include the study of low molecular weight molecules, is an emerging -omics technology useful for the identification of biomarkers. In this field, nuclear magnetic resonance (NMR) spectroscopy approach has already been used to uncover (in)fertility biomarkers in the seminal plasma (SP) of several mammalian species. However, NMR studies profiling SP metabolome to uncover in vivo fertility biomarkers are yet to be carried out in pigs. Thus, this study aimed to evaluate the putative relationship between the presence/concentration of SP-metabolites and in vivo fertility outcomes. To this end, 24 entire ejaculates (three ejaculates per boar) were collected from artificial insemination (AI)-boars throughout a year (one ejaculate every four months). Immediately after collection, ejaculates were centrifuged (1,500×g for 10 min twice) to obtain SP-samples and were stored (− 80°C) for subsequent metabolomic analysis by NMR spectroscopy. Fertility outcomes from 1,525 inseminations were recorded over a year, including farrowing rate, litter size, stillbirths per litter and the duration of pregnancy. These data were corrected to isolate the direct boar effect on each in vivo fertility parameter using a multivariate statistical model.

Results

A total of 24 metabolites were identified and quantified in all SP-samples. ROC curve analysis showed that lactate levels in SP had discriminative capacity for farrowing rate (area under the curve (AUC) = 0.764; P < 0.05) while carnitine (AUC = 0.847), hypotaurine (AUC = 0.819), sn-glycero-3-phosphocholine (AUC = 0.833), glutamate (AUC = 0.799) and glucose (AUC = 0.750) had it for litter size (P < 0.05). Similarly, citrate (AUC = 0.743), creatine (AUC = 0.812), phenylalanine (AUC = 0.750), tyrosine (AUC = 0.753) and malonate (AUC = 0.868) levels had discriminative capacity for stillbirths per litter (P < 0.05); and malonate (AUC = 0.767) and fumarate (AUC = 0.868) concentrations for gestation length (P < 0.05).

Conclusions

Considering these results, the assessment of selected SP-metabolites in ejaculates through NMR spectroscopy could be considered as a promising non-invasive tool to predict in vivo fertility outcomes in pigs. Moreover, supplementing AI-doses with specific metabolites should also be contemplated as a way to improve their fertility potential.

Early socialization and environmental enrichment of lactating piglets affects the caecal microbiota and metabolomic response after weaning

Our Publications

M. Saladrigas-García, M. D’Angelo, H. L. Ko, S. Traserra, P. Nolis, Y. Ramayo-Caldas, J. M. Folch, P. Vergara, P. Llonch, J. F. Pérez & S. M. Martín-Orúe

Scientific Reports volume 11, Article number: 6113 (2021)

ABSTRACT

The aim of this study was to determine the possible impact of early socialization and an enriched neonatal environment to improve adaptation of piglets to weaning. We hypothesized that changes in the microbiota colonization process and in their metabolic response and intestinal functionality could help the animals face weaning stress. A total of 48 sows and their litters were allotted into a control (CTR) or an enriched treatment (ENR), in which piglets from two adjacent pens were combined and enriched with toys. The pattern of caecal microbial colonization, the jejunal gene expression, the serum metabolome and the intestinal physiology of the piglets were assessed before (-2 d) and after weaning (+ 3d). A differential ordination of caecal microbiota was observed after weaning. Serum metabolome suggested a reduced energetic metabolism in ENR animals, as evidenced by shifts in triglycerides and fatty acids, VLDL/LDL and creatine regions. The TLR2 gene showed to be downregulated in the jejunum of ENR pigs after weaning. The integration of gene expression, metabolome and microbiota datasets confirmed that differences between barren and enriched neonatal environments were evident only after weaning. Our results suggest that improvements in adaptation to weaning could be mediated by a better response to the post-weaning stress.