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).

PhD Thesis: Implementation of high-resolution MRSI methods in a pre-clinical scanner, and optimization for brain longitudinal studies of therapy response in mice glioma model.

Methods & Applications, News from the SeRMN, Our Research, , ,

Last 26th July 2023 I successfully defended my PhD Thesis entitled: “PhD Thesis: Implementation of high-resolution MRSI methods in a pre-clinical scanner, and optimization for brain longitudinal studies of therapy response in mice glioma model.”

Abstract

Magnetic resonance spectroscopy and magnetic resonance spectroscopic imaging (MRS/MRSI) are non-invasive diagnostic techniques that use a strong magnetic field and radio waves to examine the chemical composition of living tissue. Working on the same principles as Magnetic Resonance Imaging (MRI), instead of producing images, MRS generates a spectrum of signals that can be used to identify the type and amount of molecules present in a tissue. The utility of MRS and MRSI has already been established in many studies, providing useful information about the chemical makeup of different regions of the brain, and allowing diagnosis of conditions such as Alzheimer’s disease, multiple sclerosis, and brain Glioblastoma (GB) tumors.

Preclinical glioblastoma studies looking forward to improving therapeutic outcomes are necessary since clinical GB has no current cure. These studies can greatly benefit from improved spatial resolution and homogeneity of the acquired MRSI grids. Hence, we can work towards improved acquisition schemes enhancing the quality of acquired data using MRS and MRSI. There exists a methodological consensus among spectroscopy experts where the Localized Adiabatic Spin Echo Refocused (semiLASER) data acquisition strategy has been ranked as the most likely localization technique to improve (pre) clinical MRS. SemiLASER uses adiabatic pulses to selectively excite and refocus the signal from a localized volume of interest in the brain. This results in a higher signal-to-noise ratio (SNR) and better spatial resolution compared to conventional data acquisition sequences.

Partial volume effects can occur in MRSI when the voxel (a 3D volume of interest) being measured contains a mixture of different neighbouring tissue types or compartments, such as grey and white matter or cerebrospinal fluid. This can lead to inaccurate quantification of metabolites, as the signal from one tissue can mix with the signal from another and affect overall pattern recorded. SemiLASER is designed to minimize partial volume effects by using adiabatic pulses to selectively excite and refocus the signal from a small region of interest within the voxel. This allows for more accurate quantification of metabolites within the region of interest, while reducing the contamination of the signal by other tissue types. In addition, semiLASER also employs an outer-volume suppression (OVS) technique to further reduce contamination from outside the region of interest. This involves using additional adiabatic pulses to selectively saturate the signal from outside the volume of interest, so that it does not contribute to the MRSI signal. Overall, the combination of selective excitation and OVS in semiLASER can help improve the accuracy of MRSI measurements and reduce partial volume effects.

Although, the clinical utility of semiLASER has been acknowledged, the pre-clinical use and implementation of semiLASER still remains a less explored area. Our group has a long record of using MRSI in therapy response monitoring of a murine model glioblastoma (the GL261 cell line) using a commercially available MRSI acquisition sequence. In our efforts towards bridging the barriers between pre-clinical and clinical research, we have implemented the clinically verified semiLASER sequence on a pre-clinical 7T Bruker Biospec USR scanner running the ParaVision 5.1 software package, which provides a graphical user interface for sequence programming and data acquisition. The single and multi-voxel semiLASER sequences were implemented with the idea that the developments generated during this PhD project will be replicable by other interested users.

The implemented SV-semiLASER and MRSI-semiLASER sequences for preclinical acquisitions were optimised to perform high resolution MRSI of living mouse brain. For this, sequences were duly verified and tested first in phantoms and later in-vivo, in wild-type (wt) and tumor bearing (GL261) mice. To do so, the Bruker pulse sequence implementation was first studied in detail to become familiar with the Bruker programming environment and a test sequence PRESS_Slice to localize the slice dimension was developed by modifying the Bruker stock PRESS sequence for single voxel localization. After careful evaluation of test sequence results, the semiLASER single and multi-voxel sequences were also implemented using a similar strategy.

The implemented SV-semiLASER sequence provided a ca. 1.4-fold improvement in SNR in phantoms and ca. 1.3-fold improvement in SNR for in-vivo subjects, in comparison to the stock Bruker PRESS (single volume acquisition) sequence. The MRSI-semiLASER sequence resulted in a ca. 1.3-fold improvement of SNR in phantoms and in-vivo subjects compared to the stock Bruker CSI-PRESS sequence. Combined with phase encoding strategies and volume reduction methods, higher spatial resolution and SNR was achieved for the implemented MRSI-semiLASER. The quantification analysis of the results was done using MATLAB based post-processing tools specially designed to process Bruker datasets and solutions for a faster post processing pipeline were proposed. The single voxel MRSI-semiLASER sequences were further simulated using NMRSCOPE-B virtual simulator, a jMRUI plug-in which positively correlated with the experimental results. Preliminary nosological images obtained using MRSI-semiLASER datasets and the SpectraClassifier tool previously developed in our group, and trained with GL261 tumors using already available CSI-PRESS data, suggested those classifiers could be robust enough to recognize the tumor region acquired with the semi-LASER sequence. Still, classifiers may require retraining for the evaluation of response to therapy, which is an ongoing project within the group.

The thesis dissertation can be downloaded in PDF format using the link below or from the official TXD and Teseo repositories (currently in progress):

Zoona Javed-PhD Thesis-Univ Autonoma Barcelona-July 2023Download

Acknowledgments

I would like to thank the financial support by the European Comission Marie Curie Initial Training Networks (ITN, call H2020-MSCA-ITN-2018, grant 813120 to project INSPiRE-MED); by the Ministry of Science and Insdustry (MCIN/AEI/10.13039/501100011033) (APC); and by Centro de Investigación Biomédica en Red—Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN http://www.ciber-bbn.es/en, CB06/01/0010), an initiative of the Instituto de Salud Carlos III (Spain) co-funded by the European Regional Development Fund (ERDF). I was recipient of a Marie Skłodowska-Curie early-stage researcher fellowship of the INSPiRE-MED project (Grant agreement ID: 813120)

Molecules with memory at room temperature

Methods & Applications

A fruitful collaboration between the Institute of Chemical Research of Catalonia (ICIQ) along with other international institutions involving the SeRMN-UAB has allowed the demonstration that a molecular magnetic memory near room temperature is a reality. A new way of storing information has come to light and possesses a potential technological impact. Molecular bits are already here.

Reference: Moneo-Corcuera, A., Nieto-Castro, D., Cirera, J., Gómez, V., Sanjosé-Orduna, J., Casadevall, C., Molnár, G., Bousseksou, A., Parella, T., Martínez-Agudo, J.M., Lloret-Fillol, J., Pérez-Temprano, M.H., Ruiz, E. & Galán-Mascarós, J.R. Molecular memory near room temperature in an iron polyanionic complex. Chem, 9, 373-393 (2023).
https://doi.org/10.1016/j.chempr.2022.09.025

More info here and in Chemistry world.

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.

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

Methods & Applications, Our Publications, , , , ,

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

Methods & Applications, News from the SeRMN, NMR Events & Courses, Our Publications, Our Research, , , , , , ,

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

Methods & Applications, Our Publications, , , ,

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.

Special Issue: NMR-Based Metabolomics

Methods & Applications, NMR Bibliography, Our Publications, Our Research, , , ,

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.

Simultaneous Enantiospecific Detection of Multiple Compounds in Mixtures using NMR Spectroscopy

Methods & Applications, Our Publications, Our Research, , , , , , , , , , , ,

Simultaneous Enantiospecific Detection of Multiple Compounds in Mixtures using NMR Spectroscopy, by Lars T. Kuhn, Kumar Motiram-Corral, Toby J. Athersuch, Teodor Parella, Míriam Pérez-Trujillo*

Angew. Chem. Int. Ed., 2020 / doi:10.1002/anie.202011727

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 analysing 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 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 characterisation.

Simultaneous enantiospecific detection of a mixture of amino acids by NMR spectroscopy

This work has been selected to be presented as a talk at 2021 scientific conferences:

· 42nd FGMR (German Chemical Society, Magnetic Resonance Section) Annual Discussion Meeting – Virtual, Sep 27 to Oct 1.

· SMASH- Small Molecule NMR Conference 2021 – Virtual, Aug 30 to Sep 2.

· Euromar 2021 Conference – Virtual, 5 to 8 July.

· 10th GERMN (Spanish NMR group of the Real Sociedad Española de Química) biennial & 9th IberoAmerican NMR Meeting – Virtual, 26 to 19 April.

Electrochemical dehalogenation of dibromomethane and 1,2‐dibromoethane to non‐toxic products using a carbon fiber brush electrode

Methods & Applications, Our Publications, Our Research, , , ,
Wiley Chemistry - उत्पादन/सेवा - १,०९१ वटा फोटोहरू | Facebook

by David Fernández‐Verdejo, Mira LK Sulonen, Míriam Pérez‐Trujillo, Ernest Marco‐Urrea, Albert Guisasola, Paqui Blánquez,  J. Chem. Technol. Biotechnol. 2020. https://doi.org/10.1002/jctb.6542

Dibromomethane (DBM) and 1,2‐dibromoethane (DBA) are two brominated volatile contaminants used in several industrial applications which are often detected in groundwater. The electrochemical degradation of DBM and DBA was studied at different cathode potentials (−0.8, −1 and −1.2 V versus Standard Hydrogen Electrode) in aqueous solution using an inexpensive graphite fiber brush electrode.

The degradation followed first‐order kinetics with respect to the nominal concentration of the brominated compounds, and the kinetic constant increased concomitantly with the decrease of the cathode potential. During the electrochemical dehalogenation 96.8% and 99.8% of the bromide in DBM and DBA was released as bromine ions, respectively. The main non‐brominated compounds detected during the degradation of DBM and DBA were methane and ethene, respectively. In addition, traces of formic acid for DBM and acetic acid for DBA degradation were detected by NMR spectroscopy. The non‐toxicity of the effluent was confirmed by a Microtox test. The efficient electrochemical degradation of DBM and DBA and the lack of toxic products open the door for a simple and non‐toxic electrochemical approach for removing aliphatic brominated compounds from aquifers and other water sources.

31P-NMR Metabolomics Revealed Species-Specific Use of Phosphorous in Trees

Methods & Applications, Our Publications, Our Research, , , , , ,

31P-NMR Metabolomics Revealed Species-Specific Use of Phosphorous in Trees of a French Guiana Rainforest, by Gargallo-Garriga, A.; Sardans, J.; Llusià, J.; Peguero, G.; Asensio, D.; Ogaya, R.; Urbina, I.; Langenhove, L.V.; Verryckt, L.T.; Courtois, E.A.; Stahl, C.; Grau, O.; Urban, O.; Janssens, I.A.; Nolis, P.; Pérez-Trujillo, M.; Parella, T.; Peñuelas, J.  Molecules 2020, 25, 3960. https://doi.org/10.3390/molecules25173960

Productivity of tropical lowland moist forests is often limited by availability and functional allocation of phosphorus (P) that drives competition among tree species and becomes a key factor in determining forestall community diversity. We used non-target 31P-NMR metabolic profiling to study the foliar P-metabolism of trees of a French Guiana rainforest. The objective was to test the hypotheses that P-use is species-specific, and that species diversity relates to species P-use and concentrations of P-containing compounds, including inorganic phosphates, orthophosphate monoesters and diesters, phosphonates and organic polyphosphates. We found that tree species explained the 59% of variance in 31P-NMR metabolite profiling of leaves. A principal component analysis showed that tree species were separated along PC 1 and PC 2 of detected P-containing compounds, which represented a continuum going from high concentrations of metabolites related to non-active P and P-storage, low total P concentrations and high N:P ratios, to high concentrations of P-containing metabolites related to energy and anabolic metabolism, high total P concentrations and low N:P ratios. These results highlight the species-specific use of P and the existence of species-specific P-use niches that are driven by the distinct species-specific position in a continuum in the P-allocation from P-storage compounds to P-containing molecules related to energy and anabolic metabolism.

This article belongs to the Special Issue:

https://www.mdpi.com/journal/molecules/special_issues/nmr_metabolomics