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Coincident with the anniversary of the demise of our colleague Noé García Almarza, Soft Matter has published one of his last research studies that has also been highlighted in the Inside Front Cover of the aforementioned journal.

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Category: Research

Ozone (O3) and hydroxyl (OH) and nitrate (NO3) radicals are the main atmospheric components that oxidize organic and inorganic pollutants, therefore affecting air quality, environmental health and climate. Measurements from the air quality monitoring network in Madrid show an increase in ozone levels of 30-40% from 2007 to 2014, while nitrogen dioxide (NO2) has dropped by 20-40%. Based on these measurements and a high spatial resolution air quality model, we estimate an average increase of 10% and 32% in OH and NO3, respectively, in Madrid, with increases of up to 70% and 90%, respectively, downtown. Our results also show a reduction of 11% in nitric acid (HNO3), which implies a considerable denoxification of the urban atmosphere and decrease of the minus 2.5 micrometre particle (PM2.5) levels. These results suggest that current NOx (NO + NO2) emission reduction policies lead to significant changes in the chemistry and the oxidative capacity of the atmosphere in and around large cities. The image shows the modelled change in OH levels between 2007 and 2014. These results have been published in Scientific Reports.

A. Saiz-Lopez, R. Borge, A. Notario, J. A. Adame, D. de la Paz, X. Querol, B. Artíñano, F. J. Gómez-Moreno & C. A. Cuevas. “Unexpected increase in the oxidation capacity of the urban atmosphere of Madrid, Spain”. Sci. Rep. (2017) 7, 45956.
DOI: 10.1038/srep45956

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Dr. Luis Cerdán, postdoctoral researcher at IQFR, has been distinguished with the “EPL Presentation Award 2017” in recognition of the best oral presentation at the IX Jornadas de Jóvenes Investigadores en Física Atómica y Molecular (J2IFAM 2017) for his work entitled “Enhanced and exotic laser performance in novel BODIPY dyes”. The prize, sponsored by the Europhysics Letters (EPL) journal, consists of a certificate and an economic reward.
The J2IFAM conferences, sponsored by the Grupo Especializado de Física Atómica y Molecular (GEFAM) of the RSEF and RSEQ, started nearly a decade ago and have run nine editions throughout the national territory. They are characteristically organized by and for young doctoral or postdoctoral researchers and intend to promote the dissemination of their research work and foster the establishment of collaborations between them.

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Myelin, the substance that forms the sheaths surrounding the axon of neurons, is an electrical insulator, and therefore is essential for the correct transmission of electrical impulses in the nervous system. The myelin sheath is particularly rich in cholesterol, galactosylceramides and sulfatides. The latter are sulfoglycolipids that can present different unsaturation and hydroxylation degrees. It is known that the nature and ratio of the different sulfatide molecular species change with age. They have also been associated with the pathogenesis of various diseases of the human Central Nervous System, including multiple sclerosis, Parkinson’s disease, leukodystrophy and Alzheimer’s disease. Consequently, these molecules could potentially be used as biomarkers of neurological diseases. However, the identification and quantification of sulfatides is a very difficult task due to their low concentrations and the high number of different molecular species. This is the reason why most of the studies only analyse the main sulfatides.
The use of liquid chromatography coupled to high-resolution tandem mass spectrometry with electrospray ionisation (LC-ESI(+)-MS/MS) has allowed us to develop an analytical method capable of carrying out a reliable identification and quantification of 37 sulfatides, many of them not detected so far. These results can be very useful in bioanalysis, due to the capability of correctly identifying these potential markers, even at concentrations of nanograms per millilitre.
This work has been possible thanks to the collaboration of researchers from IQFR, IQOG, ICTP and Cajal Institute, all of CSIC.

M. Pintado-Sierra, I. García-Álvarez, A. Bribián, E.M. Medina-Rodríguez, R. Lebrón-Aguilar, L. Garrido, F. de Castro, A. Fernández-Mayoralas, J.E. Quintanilla-López. “A comprehensive profiling of sulfatides in myelin from mouse brain using liquid chromatography coupled to high-resolution accurate tandem mass spectrometry” Anal. Chim. Acta, (2017) 951, 89-98.
DOI: 10.1016/j.aca.2016.11.054

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We have reconstructed the mercury and lead atmospheric deposition in NE Spain during the last 700 years using the concentration of these pollutants in lake sediments from the Pyrenees (Lake Montcortès). The main source of atmospheric mercury deposited in the lake is related to the mercury production in Almadén (the world´s largest mercury mine). Lead pollution is related to local mining activities in the Pyrenees and the use of leaded gasoline during the second half of the 20th century. This study highlights the sensitiveness of lake sediments to atmospheric pollution from a historical perspective.
The attached figure (linked to a bigger one) shows the Mercury (Hg) and lead (Pb) deposition rates since the 14th century, and their relationship to i) mercury production in Almadén, ii) local galena mining in the Pyrenees, and iii) the period using leaded gasoline in Europe (between 1950 and 1990).
Corella, J.P., Valero-Garcés, B.L., Wang, F., Martínez-Cortizas, A., Cuevas, C.A., Saiz-Lopez, A. “700 years reconstruction of mercury and lead atmospheric deposition in the Pyrenees (NE Spain)”. Atmospheric Environment (2017) 155, 97-107. (doi: 10.1016/j.atmosenv.2017.02.018)

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The mechanism of the β-lactam antibacterials is the functionally irreversible acylation of the enzymes that catalyze the cross-linking steps in the biosynthesis of their peptidoglycan cell wall. The Gram-positive pathogen Staphylococcus aureus uses one primary resistance mechanism based on an enzyme, called penicillin-binding protein 2a (PBP2a), which is involved in this biosynthetic pathway being able to discriminate effectively against the β-lactam antibiotics as potential inhibitors, and in favor of the peptidoglycan substrate. The basis for this discrimination is an allosteric site, distal from the active site, that when properly occupied concomitantly opens the gatekeeper residues within the active site and realigns the conformation of key residues to permit catalysis. Throughout a combination of different techniques (X-ray crystallography and computational analysis by molecular dynamics and quantum mechanics), our results provide critical information about the regulation mechanism of PBP2a, a key protein in the primary resistance mechanism against antibiotics, giving us detailed information about the structural basis of communication between the allosteric and catalytic sites. Furthermore, this study reveals how β-lactam antibiotics mimicry the peptidoglycan substrates, as foundational to the mechanistic understanding of emerging PBP2a resistance mutations. This is part of a collaborative effort between the IQFR and the Univ. of Notre Dame (Indiana, USA).

Mahasenan, K.; Molina, R.; Bouley, R.; Batuecas, M.; Fisher, J.; Hermoso, J.A.; Chang, M. and Mobashery*, S. “Conformational dynamics in penicillin-binding protein 2a of methicillin-resistant Staphylococcus aureus, allosteric communication network and enablement of catalysis”. J. Am. Chem. Soc. (2017).
DOI: 10.1021/jacs.6b12565

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The oriented attachment of molecules in general and proteins in particular at the interface of nanoparticles is currently a challenge in (bio)nanotechnology. In this work carried out by research groups of the Institute of Physical Chemistry Rocasolano, Institute of Material Science of Madrid and Institute of Catalysis and Petroleochemistry, agarose-coated magnetic nanoparticles have been prepared and characterized. They have shown that these nanoparticles constitute an excellent experimental platform for the oriented attachment of recombinant proteins tagged with the β-trefoil lectin LSL150. Optimization of the preparation of the agarose-coated magnetic nanoparticles as followed by a survey of techniques such as dynamic light scattering (DLS), Fourier transform infrared spectroscopy (FTIR) and thermogravimetric studies, required the decoupling of particle formation from agarose coating. LSL150 interacted with these agarose-coated nanoparticles exclusively through the recognition of the sugars of the polymer, forming highly stable complexes. The marked topological polarity of this small lectin makes it an excellent molecular adaptor for the oriented attachment of proteins at the nanoparticle interface since they always face the bulk solvent. This fact opens up new possibilities for the design of novel and more efficient (bio)sensors.

Iván Acebrón, Amalia G. Ruiz-Estrada, Yurena Luengo, María del Puerto Morales, José Manuel Guisán, and José Miguel Mancheño. “Oriented Attachment of Recombinant Proteins to Agarose-Coated Magnetic Nanoparticles by Means of a β‑Trefoil Lectin Domain”. Bioconjugate Chemistry (2016) 27, 2734−2743.
(doi:10.1021/acs.bioconjchem.6b00504)

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Apoptin is a small protein from the chicken anemia virus‎ which selectively induces apoptosis (programmed cell suicide) in over 80 different cancer cell lines, yet does not harm healthy cells. Apoptin is a promising cancer lead and is progressing through clinical trials. Nevertheless, Apoptin's strong tendency to oligomerize limits its ability to enter cells and thwarts studies of its structure. Therefore, we have prepared and characterized a monomeric Apoptin variant that retains most of the wild type protein's selective anti-cancer activity. Using NMR spectroscopy, this variant was shown to be intrinsically disordered and dynamic on ps-ms time scales. The conformational ensemble is not significantly affected by specific phosphorylation, addition of Mg++, pH changes or red/ox conditions. These findings support a model for Apoptin's mechanism of action in which cancer specific kinases phosphorylate Apoptin, leading to its accumulation in the nucleus and activation of p53-independent apoptosis.

Referencias:

1. "Insights into the mechanism of Apoptin's exquisitely selective anti-tumor action from atomic level characterization of its conformation and dynamics." Ruiz-Martínez S, Pantoja-Uceda D, Castro J, Vilanova M, Ribó M, Bruix M, Benito A, Laurents DV. Arch Biochem Biophys. (2017) 614:53-64.
doi:10.1016/j.abb.2016.12.010

2. "A truncated Apoptin protein variant selectively kills cancer cells." Ruiz-Martínez S, Castro J, Vilanova M, Bruix M, Laurents DV, Ribó M, Benito A. Invest New Drugs (2017).
doi:10.1007/s10637-017-0431-6