Category Archives: News from the SeRMN

News about the SeRMN that do not fit in any other of the available categories.

MRI/MRS in treated Alzheimer mice

Differential effects of apoE and apoJ mimetic peptides on the action of an anti-Aβ scFv in 3xTg-AD mice” by L. Montoliu-Gaya, J. Güell-Bosch, G. Esquerda-Canals, A.R. Roda, G. Serra-Mir, S. Lope-Piedrafita, J.L. Sánchez-Quesada, S. Villegas. Biochem Pharmacol. 2018, 155:380-392. DOI: 10.1016/j.bcp.2018.07.012.

Anti-Aβ immunotherapy has emerged as a promising approach to treat Alzheimer’s disease (AD). The single-chain variable fragment scFv-h3D6 is an anti-Aβ antibody fragment that lacks the Fc region, which is associated with the induction of microglial reactivity by the full-length monoclonal antibody bapineuzumab. ScFv-h3D6 was previously shown to restore the levels of apolipoprotein E (apoE) and apolipoprotein J (apoJ) in a tripletransgenic- AD (3xTg-AD) mouse model. Since apoE and apoJ play an important role in the development of AD, we aimed to study the in vivo effect of the combined therapy of scFv-h3D6 with apoE and apoJ mimetic peptides (MPs).

Magnetic Resonance Imaging showed a general tendency of the different treatments to protect against the reduction in brain volume. This protection was further suggested by MRS, since all the treatments tended to recover the levels of Ala, which is involved in the alanine-glucose cycle, and NAA, which is a marker for cell viability. All the treatments in the present work recovered the IL-33 levels, and apoE-MP showed a potent anti-inflammatory effect in terms of glial activation that was decreased in the presence of scFv-h3D6, whereas the combination of apoJ-MP and scFvh3D6 was not detrimental. Moreover, the endogenous apoE and apoJ levels were decreased by scFvh3D6, but the MPs induced a simultaneous increase in both apolipoproteins, which reflects a coordinated expression between them.

PhD Thesis: Development of Resolution-Enhanced NMR Techniques for Improved Small Molecules Structural Analysis

Last July 14th 2018 Núria Marcó defended her PhD Thesis entitled: Development of Resolution-Enhanced NMR Techniques for Improved Small Molecules Structural Analysis

 

The present doctoral thesis is framed within the field of Nuclear Magnetic Resonance (NMR) spectroscopy.

NMR spectroscopy is an analytic technique and, therefore, one of its main objectives is to unravel the correct structure of the molecules analyzed.This present doctoral thesis  is focused on this main objective. This work consists in a compendium of 7 publications, written in several prestigious scientific journals, that develop in depth the efficient and accurate determination of the constitution, configuration and conformation of small molecules thanks to the application of resolution improvements techniques.

In order to do that it is studied the accurate and efficient measurement of isotropic (homo- and heteronuclear scalar coupling constants) for the 2D structre determination, as well as the anisotropic parameters (RDCs, RCSAs and RQCs) for the 3D structure analysis. These anisotropic parameters allows us the discrimination of the different conformers of a molecule and can be found in weakly alignment media. PMMA gel provides an easy, reusable, and practical way to obtain this weakly alignment media. In this work, It has been researched the best way to get these anisotropic parameters, developing and adapting new pulse sequences to this type of media.

To get the correct structure (2D and 3D) it is important to obtain a precise and accurate measurement. In this thesis the great accuracy of isotropic and anisotropic parameters has been achieved through the use of resolution improvement techniques such as Pure-Shift, Spectral Aliasing and Non Uniform Sampling.

In addition it has been applied protocols for the easy automatization and measurement of coupling constants in isotropic and anisotropic media.

Also it has been design improved pulse sequences to achieve the measurement of longer- range heteronuclear connectivities that will  increase the amount of information that we will have available to do the structural analysis

Each experiment has been discussed from a methodological point of view. An assessment on its application has been also performed.

Pulse Programs and Data Set Examples:

Publication 1:
Extending long-range heteronuclear NMR connectivities by HSQMBC-COSY and HSQMBC-TOCSY experiments Saurí, J.; Marcó, N.; Williamson, R. T.; Martin, G. E.; Parella, T. J. Magn. Reson. 2015, 258, 25–32.
DOI 10.1016/j.jmr.2015.06.004

Pulse Program Code for Bruker:

Data set Example:

 

Publication 2:
Ultra high-resolution HSQC: Application to the efficient and accurate measurement of heteronuclear coupling constants  Marcó, N.; Fredi, A.; Parella, T. Chem. Commun. 2015, 51 (15), 3262–3265.
DOI 10.1039/C4CC10279G

Pulse Program Code for Bruker:

Data set Example:

 

Publication 3:
Isotropic/Anisotropic NMR Editing by Resolution-Enhanced NMR Spectroscopy Marcó, N.; Gil, R. R.; Parella, T. ChemPhysChem 2018, 19, 9, 1024-1029.
DOI: 10.1002/cphc.201800094

Pulse Programs Code for Bruker:

 

Publication 4:
Structural discrimination from in situ measurement of 1DCH and 2DHH residual dipolar coupling constants Marcó, N.; Gil, R. R.; Parella, T. Magn. Reson. Chem. 2017, 55 (6), 540–545.
DOI 10.1002/mrc.4575

Pulse Programs Code for Bruker:

Data set Example:

 

Publication 5:
Perfect 1JCH-resolved HSQC: Efficient measurement of one-bond proton-carbon coupling constants along the indirect dimension Marcó, N.; Souza, A. A.; Nolis, P.; Gil, R. R.; Parella, T. J. Magn. Reson. 2017, 276, 37–42.
DOI: 10.1016/j.jmr.2017.01.002

Pulse Programs Code for Bruker:

Data set Example:

 

Publication 6:
1JCH NMR Profile: Identification of key structural features and functionalities by visual observation and direct measurement of one-bond proton-carbon coupling constants Marcó, N.; Souza, A. A.; Nolis, P.; Cobas, C.; Gil, R. R.; Parella, T. J. Org. Chem. 2017, 82 (4), 2040–2044.
DOI: 10.1021/acs.joc.6b02873

Pulse Programs Code for Bruker:

 

Publication 7:
2JHH-resolved HSQC: Exclusive determination of geminal proton-proton coupling constants Marcó, N.; Nolis, P.; Gil, R. R.; Parella, T. J. Magn. Reson. 2017, 282, 18–26.
DOI: 10.1016/j.jmr.2017.06.014

Pulse Programs Code for Bruker:

 

11th Workshop on Magnetic Resonance Spectroscopy and Imaging (MRI/MRS) Applied to Laboratory Animals

Workshop dates: June 25th – 28th, 2018
Registration deadline: June 10th, 2018
Registration:   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.

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

NEW BOOK RELEASE: “Preclinical MRI methods and protocols”

“Preclinical MRI: Methods and Protocols” by Maria Luisa Garcia Martin and Pilar Lopez Larrubia (Editors). Part of the Methods in Molecular Biology book series (MIMB, volume 1718). DOI: 10.1007/978-1-4939-7531-0.

This book was conceived with the idea of providing an update on a wide variety of preclinical MRI methods and protocols to help technicians and researchers interested in this technology. The basics of MRI physics are introduced, followed by chapters describing updated methodology and protocols for some standard and more advanced MRI techniques covering diffusion, perfusion, functional imaging, in-vivo spectroscopy (proton and heteronuclear), susceptibility contrast MRI… The book also contains some chapters where some applications of those methods are illustrated in animal models of several diseases including cancer, stroke and neurodegeneration. Protocols are described in a step-by-step approach, with interesting notes and tips at the end of each chapter, which -a priori- should allow the new worker to obtain successful results with the first attempt ;o) .

PhD Thesis: Edició crítica dels escolis al cant IX de l’Odissea, by Esperança Ramírez Sevilla

Last December, Esperança Ramírez, our facility secretary, defended her PhD Thesis entitled: “Edició crítica dels escolis al cant IX de l’Odissea” (Critical Edition of the Scholia to the Odyssey Book IX). The thesis defense took place at 11am on Friday 16 December in the Facultat de Filosofia i Lletres of Universitat Autònoma de Barcelona.

Scholia (singular scholium or scholion, from Ancient Greek: σχόλιον, “comment, interpretation”) are grammatical, critical, or explanatory comments, either original or extracted from pre-existing commentaries, which are inserted on the margin of the manuscript of an ancient author, as glosses.
Scholia definition in the Wikipedia

In her doctoral dissertation she does a thorough, critical and updated edition of the scholia to the Odyssey Book IX, including the scholia regarded as minor as well as the major scholia. This book and the following three books are collectively referred to as the apologoi: Odysseus’ “stories”, and they have attracted the attention of scholars of Homer works of all times.

To carry out her research work, she had to systematically analyse and challenge previous editions that, in full or in part, included scholia from the Odyssey Book IX, and, on the other hand, she had to decide the corpus of manuscripts that she would study, which was finally set to 37 from different typologies and genetic filiations.

Odyssey greek manuscript
Example of a handwritten manuscript studied in this thesis, the text of the Odyseey is on the left column, major scholia (comments) are on the right column, and minor scholia are interspersed in between the lines of the Odyssey text.

It stands out the methodological novelty of classifying the scholia according to their content: related to the titles, dedicated to argument summaries, focused on lexicographic aspects, contextual or mythographic. This classification, on top of helping to understand the content of each scholium, offers too an interesting view of the filiation of manuscripts.

Her goal was to offer a body of data encompassing the scholia, the annotations and also the most significant corrections of the Homeric text. In that corpus there are several types of content, from multiple versions of myths to words that must be construed, including syntactic expressions or morphological annotations.

The thesis is available for download from TESEO, the official repository of Spanish doctoral dissertations.

A translation of the Odyssey to English by A.T. Murray (1919) can be read on-line at the Classical Texts Library and another translation by Samuel Butler at The Internet Classics Archive. Also, if you are curious, you can hear how Homer’s Odyssey sounded in the original ancient greek, and if you dare so, you can take a free 64-lessons course to learn ancient greek.

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.

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.

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.