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).

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

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

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

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

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

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

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

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 202025, 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

In vivo MRI/MRS longitudinal study of immunotherapy in Alzheimer’s

Progression of Alzheimer’s disease and effect of scFv-h3D6 immunotherapy in the 3xTg-AD mouse model: An in vivo longitudinal study using Magnetic Resonance Imaging and Spectroscopy by Güell-Bosch J, Lope-Piedrafita S, Esquerda-Canals G, Montoliu-Gaya L, and Villegas S. NMR in Biomedicine 33(5):e4263; DOI: 10.1002/nbm.4263.

Alzheimer’s disease (AD) is an incurable disease that affects most of the 47 million people estimated as living with dementia worldwide. The main histopathological hallmarks of AD are extracellular β-amyloid (Aβ) plaques and intracellular neurofibrillary tangles (NFTs) composed of hyperphosphorylated tau protein.  In recent years, Aβ-immunotherapy has been revealed as a potential tool in AD treatment. One strategy consists of using single-chain variable fragments (scFvs), which avoids the fragment crystallizable (Fc) effects that are supposed to trigger a microglial response, leading to microhemorrhages and vasogenic edemas, as evidenced in clinical trials with bapineuzumab. The scFv-h3D6 generated by our research group derives from this monoclonal antibody, which targets the N-terminal of the Aβ peptide and recognizes monomers, oligomers and fibrils.

In this study, 3xTg-AD mice were intraperitoneally and monthly treated with 100 μg of scFv-h3D6 (a dose of ~3.3 mg/kg) or PBS, from 5 to 12 months of age (-mo), the age at which the mice were sacrificed and samples collected for histological and biochemical analyses. During treatments, four monitoring sessions using magnetic resonance imaging and spectroscopy (MRI/MRS) were performed at 5, 7, 9, and 12 months of age. MRI/MRS techniques allow, in a non-invasive manner, to draw an in vivo picture of concrete aspects of the pathology and to monitor its development across time. Compared with the genetic background, 3xTg-AD mice presented a smaller volume in almost all cerebral regions and ages examined, an increase in both the intra and extracellular Aβ1-42 at 12-mo, and an inflammation process at this age, in both the hippocampus (IL-6 and mIns) and cortex (IL-6). In addition, treatment with scFv-h3D6 partially recovered the values in brain volume, and Aβ, IL-6, and mIns concentrations, among others, encouraging further studies with this antibody fragment.

A new strategy for the regioselective functionalization of C60 fullerenes

Supramolecular Fullerene Sponges as Catalytic Masks for Regioselective Functionalization of C60“, by Carles Fuertes-Espinosa, Cristina García-Simón, Míriam Pujals, Marc Garcia-Borràs, Laura Gómez, Teodor Parella, Judit Juanhuix, Inhar Imaz, Daniel Maspoch, Miquel Costas and Xavi Ribas.

Chem, in press (2020). DOI: 10.1016/j.chempr.2019.10.010

The supramolecular mask protocol is a significant step forward for the regioselective functionalization of fullerenes. The exquisite ability to form pure-isomer poly-functionalized C60 adducts, overcoming tedious and non-practical chromatographic separations, allows for their direct testing in solar cell prototypes. Furthermore, the supramolecular mask strategy can be applied to C70 or higher fullerenes, opening a plethora of poly-functionalized fullerene derivatives to be synthesized and tested. Moreover, apart from the nucleophilic cyclopropanations reported herein, the protocol is currently being expanded to Diels-Alder (DA), 1,3-dipolar cycloadditions and PC60BM-type cyclopropanations, thus enabling a variety of regioselective functionalization reactions. This supramolecular mask strategy can help the discovery of the next generation of improved solar cells (organic or perovskite based) or new drug candidates.

This research has been carried out in close collaboration with Dr. Xavi Ribas (from the QBIS-CAT research group of the University of Girona (UdG)), the Catalan Institute of Nanotechnology (ICN2), the ALBA-BCN synchrotron and the NMR Service of the Autonomous University of Barcelona ( UAB). The results have just been published in the online version of the prestigious CHEM scientific journal .

Recyclable Mesoporous Organosilica Nanoparticles (MSN) for Asymmetric Organocatalysis

Li, Hao, Míriam Pérez-Trujillo, Xavier Cattoën & Roser Pleixats. 2019. Recyclable Mesoporous Organosilica Nanoparticles Derived from Proline-Valinol Amides for Asymmetric Organocatalysis. ACS Sustainable Chemistry & Engineering 7(17). 14815-14828. DOI: 10.1021/acssuschemeng.9b02838

This is the first report on the obtention of functionalized MSN by a co-condensation procedure with a structurally complex chiral precursor. The functionalized MSN have been characterized by elemental analysis, 29Si and 13C CP MAS NMR, transmission electron microscopy, scanning electron microscopy, N2-sorption measurements, dynamic light scattering, ζ-potential, and powder X-ray diffraction. We have evaluated the activity of these materials as recyclable catalysts in the asymmetric aldol reaction. The use of organosilica nanoparticles reduces the problems of diffusion and low reaction rates encountered with bulk organosilicas.