Category Archives: News from the SeRMN

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

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

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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.

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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

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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 Parellaand 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.

André Fredi’s oral presentation at 8th GERMN / 5th Iberian NMR Meeting

André Fredi made an oral presentation at the 8th GERMN / 5th Iberian NMR Meeting (GERMN 2016) held in Valencia, Spain from 27th to 29th June 2016.

In his presentation, that was titled  Exploring the use of Generalized Indirect Covariance to reconstruct Pure Shift NMR spectra: Current Pros and Cons”, André explained how to make pure spectra shift from Generalized Indirect IMG-20160628-WA0028Covariance processing (psGIC). This new method is basically a new way to get “synthetic” pure shift spectra without the need to purchase a pure shift spectrum in the spectrometer and without the penalties that pure-shift experiments cause.

André has been working as a Ph.D. candidate at the Department of Chemistry and SeRMN under the direction of Dr. Teodor Parella and Dr. Pau Nolis since November 2014, when he enrolled in the Department of Chemistry doctoral program at Universitat Autònoma de Barcelona with a fellowship from CNPq-Brazil. He is currently in his second year and expects to defend the doctoral thesis on 2017/2018.

 

Presentations at the EUROMAR 2016 Conference

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André Fredi (PhD student) and Teodor Parella presented our last research works at the annual meeting of the European magnetic resonance community EUROMAR 2016 Conference that was celebrated on days 3th to 7th July in Aarhus, Denmark. Find below a summary of our contributions. Continue reading Presentations at the EUROMAR 2016 Conference

Exploring the use of Generalized Indirect Covariance to Reconstruct Pure shift NMR Spectra: Current Pros and Cons.

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Title: Exploring the use of Generalized Indirect Covariance to Reconstruct Pure shift NMR Spectra: Current Pros and Cons.
Authors: André Fredi, Pau Nolis, Carlos Cobas, Gary E. Martin and Teodor Parella.
DOI: 10.1016/j.jmr.2016.03.003

ABSTRACT: The current pros and cons of a processing protocol to generate pure chemical shift NMR spectra using Generalized Indirect Covariance are presented and discussed. The transformation of any standard 2D homonuclear and heteronuclear spectrum to its pure shift counterpart by using a reference DIAG spectrum is described. Continue reading Exploring the use of Generalized Indirect Covariance to Reconstruct Pure shift NMR Spectra: Current Pros and Cons.

Visiting PhD Student Yaoyao Wang

Blog2Today we are saying goodbye to our dear Yaoyao, though we hope to see her very soon again.

Yaoyao is currently finishing her PhD on metabonomics applied to clinical biomarkers in the Legido-Quigley Lab at King’s College London (KCL).

She has been visiting us for the last two months, during which we have been working together in two metabonomics projects related to drug misuse biomarkers and chiral metabonomics. It has been a great pleasure for us to spend this time with her and continue with this collaboration from now on.