Shifts in plant foliar and floral metabolomes in response to the suppression of the associated microbiota

logo_BMCPB

“Shifts in plant foliar and floral metabolomes in response to the suppression of the associated microbiota” by A. Gargallo-Garriga, J. Sardans, M. Pérez-Trujillo, A. Guenther, J. Llusià, L. Rico, J. Terradas, G. Farré-Armengol, I. Filella, T. Parella and J. Peñuelas. BMC Plant Biology 2016; 16:78. DOI: 10.1186/s12870-016-0767-7

The significance of microbial populations to the health and physiology of human and animal hosts has become a burgeoning and increasingly newsworthy topic. Of course, plants are also hosts for microbial life, and our metabolomics new study in BMC Plant Biology suggests that microbial influence on plant biology is more complex than we currently appreciate. When elderflower plants were treated with antibiotics, metabolic changes occurred not only at the sites of microbial colonization – the leaf and flower – but also in internal organs. These results demonstrate key contributions to local metabolic activity of microbes on elderflower leaves and flowers, and suggest that – as seen in other organisms – microbial activity can have a systemic impact host biology.

Fig1_BMCPB_AGG

Optimized polarization build-up times in dissolution DNP-NMR using a benzyl amino derivative of BDPA

RA.indt

“Optimized polarization build-up times in dissolution DNP-NMR using a benzyl amino derivative of BDPA” by José Luis. Muñoz Gómez, Eva Monteagudo, Vega LLoveras, Teodor Parella, Jaume Veciana and José Vidal Gancedo. RSC Advances, 2016, 6, 27077. DOI: 10.1039/c6ra00635c

 

The synthesis of two novel BDPA-like radicals, a benzyl amino (BAm-BDPA, 7) and a cyano (CN-BDPA, 5) derivative, is reported and their behaviour as polarizing agents for fast dissolution Dynamic Nuclear Polarization (DNP) is evaluated. The radical 7 is a promising candidate for DNP studies since it is soluble in neat [1-13C]pyruvic acid (PA), and therefore the use of an additional glassing agent for sample homogeneity is avoided. In addition, a 60 mM sample of 7 offers optimum 13C NMR signal enhancements using fairly short polarization times (about 1800 s). It is shown that DNP-NMR measurements using 7 can be performed much more efficiently in terms of the signal enhancement per polarization build-up time unit than when using the reference OX63 or BDPA radicals. These enhanced features are translated to a substantial reduction of polarization times that represents an optimum temporary use of the DNP polarizer and allow economized liquid helium consumption.

Figura_blog_BAm_BDPA

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

JMR

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. Reconstructed pure shift NMR spectra of NOESY, HSQC, HSQC-TOCSY and HSQMBC experiments are reported
for the target molecule strychnine.graphical abstract

 

TUTORIAL:
TUTORIAL psGIC

VÍDEO:

http://audioslides.elsevier.com//ViewerLarge.aspx?source=1&doi=10.1016/j.jmr.2016.03.003

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.

Seminar: Biomarker and metabolomics, a novel approach to detect drug misuse

Yaoyao Wang, visiting PhD student from King’s College London, will be giving a talk on  December the 18th at 10:00 h in the SeRMN. Her talk is entitled “Biomarker and metabolomics: a novel approach to detect drug misuse”.

yaoyao

Yaoyao is from Clinical Biomarkers Lab of the Institute of Pharmaceutical Science, King’s College London (KCL). Her PhD project focuses on developing metabolomics approach to identify biomarkers for drug misuse through the analysis of human biofluids samples and the development of data treatment methods, using R (XCMS) and other bioinformatics tools. She has been collaborating intensively with the Drug Control Centre of KCL using LC-MS.

Her talk will include the metabolomics biomarker discovery of low dose salbutamol in urine collected for anti-doping tests and preliminary longitudinal metabolomics study of “date-rape” drug GHB, as well as a glance of the other on-going projects in Clinical Biomarkers Lab.

All interested people are welcome to attend this seminar.

SeRMN gets a visit of Gustavo G. Simamoto from UNICAMP-Brazil

AvMmMO19F-_NOP6OnHN_BVnx8QEv3yIaDjCf-B76l4EEWe received a visit from Gustavo Giraldi Shimamoto who is PhD student and technical NMR at University of Campinas (UNICAMP-Brazil). Gustavo was one month (November 2015) in our laboratory learning a little about how our NMR service works, the type of service we provide both to universities and to companies and some of our routine work. In addition, Gustavo learned about pulse sequence, modern NMR experiments as pure-shift and HSQMBC. For us it was a great pleasure to receive and meet Gustavo.

SeRMN at the SMASH NMR 2015 Conference

Some of our last research works has been presented at the annual meeting of the SmallMolecule NMR Conference (SMASH) that has been taken place in Baveno (Italy) from 20thto 24thSeptember 2015.

Find below a summary of our contributions.

Núria Marcó presented two posters.

 

Poster nº 25: “Ultra high-resolution HSQC: application to the efficient and accurate measurement of heteronuclear coupling constants”. Núria Marcó, Andre Fredi and Teodor Parella.

Abstract: Digital resolution and signal resolution are two important concepts in multidimensional NMR spectroscopy. One of the more critical parameters defining the total acquisition time of a 2D NMR experiment is the number of variable t1evolution times required to achieve a satisfactory digital resolution in its indirect F1 dimension. In this study, the success of implementing spectral aliasing along the indirect F1 dimension of HSQC experiments is demonstrated by the easy measurement of heteronuclear coupling constants from the indirect dimension of 2D HSQC spectra, without any significant increase of the experimental time. It is also shown that the gains of introducing aliasing are further improved with the large signal resolution achieved by the collapse of the J(HH) multiplet structure by broadband 1H homodecoupling in the F2 dimension. The resulting 2D cross-peaks exhibit ultra simplified multiplet patterns from which the measurement of the active J values is determined in a straightforward manner. Experimental data will be provided for the simultaneous determination of the magnitude and the sign of J(CX) and J(HX) coupling constants (X = 19F, 31P or 2H).

Poster nº 26: “Extending long-range heteronuclear NMR connectivities by modified HSQMBC experiments”. Josep Saurí, Núria Marcó, R. Thomas Williamson, Gary E. Martin and Teodor Parella.

Abstract: The detection of long-range heteronuclear correlations associated with J(CH) coupling values smaller than 1-2 Hz is a challenge in the structural analysis of small molecules and natural products. LR-HSQMBC, HSQMBC-COSY and HSQMBC-TOCSY pulse schemes are evaluated as complementary NMR methods to standard HMBC/HSQMBC experiments. The re-optimization of the interpulse delay and the incorporation of an additional J(HH) transfer step in the HSQMBC pulse scheme can favor the sensitive observation of traditionally missing or very weak correlations and, in addition, facilitates the detection of a significant number of still longer-range connectivities to both protonated and non-protonated carbons under optimal sensitivity conditions. A comparative 1H-13C study is performed using strychnine as a model compound and several examples are also provided including 1H-15N applications.
AqmuMUJcsjzx4RiuGwJemZbuPnxoxjcjWKKI5YF9CB1M

 

PhD Thesis Defense: Metabolomics and stoichiometry adapted to the study of environmental impacts on plants. PhD Thesis by Albert Gargallo Garriga

 

I am defending my PhD thesis next Thursday (September 10, 2015) at 11.30am in the Sala d´Actes “Carles Miravitlles” of the Institut de Ciències de Materials de Barcelona (ICMAB), Campus UAB. The title of my thesis is “Metabolomics and stoichiometry adapted to the study of environmental impacts on plants” and below you can find an abstract of the work. If you are interested you are very welcome.

 

Portada

 

Metabolomics has allowed significant advances in biological sciences. An increasing number of ecological studies have applied a metabolomic approach to answer ecological questions (ecometabolomics) during the last few years. The work developed throughout this PhD thesis means a further step in the field of ecometabolomics.

The first chapter of results of this thesis is dedicated to the adaptation of a previously described protocol to conduct metabolomics in ecological studies. It describes in detail the procedures to follow, in the field and in the laboratory, to perform metabolomic analyses using nuclear magnetic resonance (NMR) spectroscopy and liquid chromatography-mass spectrometry (LC-MS) coupled to stoichiometric analysis. This improvement allowed combining the study of ecological stoichiometry and metabolomics in a single protocol and obtaining a wider overview of what is happing to the organism.

In the second and third chapters, the described protocol is applied to study how some climate change factors (drought, warming and irrigation) affect different organs of the plant (shoots and roots of Holcus lanatus and Alopecurus pratensis) at two different seasons. The results show a relationship between the metabolic variation observed in roots and the observed in shoots. The simultaneous metabolomic analysis of both organs of these grasses provide a complete view of the entire plant; including the response of different organs to environmental changes, the global phenotypic response and the metabolic mechanisms underlying these responses.

The fourth chapter is dedicated to the study of the simulated attack to Quercus Ilex leaves by an herbivore. The results show differences in the 1H NMR metabolic profiles of the leaf before and after the wound. A marked increase in C-rich secondary metabolites, quinic acid and quercitol, which are related to the shikimic metabolic pathway, was observed. The results also confirm that quinic acid and quercitol are present in great content in the genus Quercus and they are involved in mechanisms against biotic stress.

In the fifth chapter a study of the relationship between the epiphytic microorganisms and the plant host is described. This study highlights the large complexity of the episphere, the existence of internal microbial communities and the strong relationships between the structure and function of the internal and external plant metabolomes. These results warrant further study of the specific relationships between plants and the microbial communities living on and in them.

Storage properties of the Li-N-H system

hydrogen_energy“Role of aluminum chloride on the reversible hydrogen storage properties of the Li-N-H system”

Fernández, L.; Garroni, S.; Larochette, P.; Nolis, P.; Mulas, G.; Enzo, S.; Baró, M.D.; Gennari, F. International Journal of Hydrogen Energy, IN PRESS 2015 doi:10.1016/j.ijhydene.2015.08.030

 In order to understand the role of AlCl3 addition on the Li–N–H system, we have systematically investigated the hydrogen sorption kinetics and the reactions between LiNH2–LiH and AlCl3 additive with a multitechnique approach involving differential scanning calorimetry (DSC), hydrogen volumetric measurements, X-ray powder diffraction (XRPD), Fourier transform infrared analysis (FTIR) and solid-state nuclear magnetic resonance (NMR). Different interactions were identified as a function of the amount of added AlCl3. For low AlCl3 addition (0.03 mol), the Al3+ is incorporated into the interstitial sites by the LiNH2 structure. When AlCl3 amount increased (0.08 and 0.13 mol), the formation of new amide-chloride phases were detected by XRPD and indexed with cubic and hexagonal Li–Al–N–H–Cl geometries. Occurrence of such new phases was also confirmed by FTIR and NMR. The formation of these new Li–Al–N–H–Cl phases modifies the kinetics as well as the thermodynamic behavior of the original Li–N–H system. Interesting, in all AlCl3-doped composites, hydrogen was stored reversibly with faster sorption kinetics than un-doped Li–N–H system and with a significant reduction of NH3 emission. This improvement can be associated with the Al3+ incorporation into LiNH2 that promotes the migration of Li+, while for high AlCl3 doping, the formation of new phases Li–Al–N–H–Cl also weakens the N–H bond.

Microsoft Word - Role of aluminum chloride_with Figures_final_Ju

PhD Thesis: Development and application of modern pure shift NMR techniques and improved HSQC and HSQMBC experiments

Last 16st July 2015 I defended my PhD Thesis entitled: Development and application of modern pure shift NMR techniques and improved HSQC/HSQMBC experiments.

Presentación1

The present doctoral thesis is framed within the Nuclear Magnetic Resonance (NMR) spectroscopy field, more specifically in the design of modern NMR methodologies. The research work carried out is focused on the design and application of new and modern NMR methodologies (i) to perform efficient broadband 1H homodecoupling in 1D/2D NMR experiments and (ii) to accurately determine homo- and heteronuclear coupling constants in isotropic and anisotropic conditions through improved HSQC and HSQMBC-type experiments. The thesis is presented as a compendium ten (10) publications that have been published in several peer-reviewed international scientific journals as original research papers.

Several 1H homodecoupled NMR experiments have been developed along this doctoral thesis. Most of them are based on the Homodecoupled Band-Selective (HOBS) experiment through which it is possible to obtain homodecoupled NMR spectra with full sensitivity. HOBS methods offer a powerful and simple way to obtain high-resolved 1D and 2D NMR spectra, as efficiently demonstrated for the accurate, simple and direct measurement of T1/T2 relaxation times in overlapped regions, the determination of heteronuclear coupling constants from simplified multiplets, the determination of very small chemical shift differences with success application in enantiodifferentation studies or the analysis of highly complex mixtures. In addition, the concept of ultra-high-resolution NMR spectroscopy has been tested by combining several resolution-enhanced techniques into a single NMR experiment.

On the other hand, for many years the measurement and practical use of coupling constants have been a timely topic but there are still a number of unresolved issues. Along this doctoral thesis a suite of robust HSQC and HSQMBC experiments have been developed which provide accurate and precise measurements of couplings constants through simple and direct analysis of cross-peaks without involving complex post-processing data manipulation.

Useful Links: Pulse Programs and Data Set Examples