News Article | May 19, 2017
The annual mortality rate in childhood cancer of the sympathetic nervous system, or neuroblastoma, is 10 per million between the ages of 0 and 4. The collaborative work between Basque and Valencian researchers has served to identify some genetic mutations that will help to improve the treatment of this disease. Researchers at the Instituto de Investigación Sanitaria La Fe (Institute of Healthcare Research La Fe) in Valencia led by Jaime Font de Mora, in collaboration with José Luis Zugaza, an Ikerbasque researcher at the UPV/EHU-University of the Basque Country and the "Achucarro Basque Center for Neuroscience," have by means of NGS (Next Generation Sequencing) identified mutations in the Tiam1 gene that predict a better prognosis for neuroblastoma patients. A neuroblastoma is a solid, extracranial tumor more frequent in childhood. It accounts for 7% of all paediatric cancers and is the cause of 15% of the total number of deaths resulting from oncological processes in childhood. The incidence of it ranges between 8 and 10 cases per million children. Family cases of neuroblastoma have been described but they are extremely rare. Right now, it is not known how this rare type of cancer originates. The study reveals that these mutations that anticipate the progression of this disease are located in various Tiam1 domains related to the Ras and Rac GTPases and also with Myc; all these proteins are involved in the aetiology and progression of this type of cancer. The results have been published in the journal Oncotarget, which specialises in works dealing with targets for different types of cancers. These results suggest that the signalosome controlled by Tiam1 may be essential in the development of the neuroblastoma and, therefore, Tiam1 is positioned as a target that could help to improve the effectiveness of neuroblastoma treatment. The next step is to incorporate these studies into clinical practice to improve the tools and procedures in the diagnosis with a view to implementing earlier treatments for the children affected.
News Article | April 25, 2017
Plants need nitrogen to grow, and intensive agriculture requires the input of nitrogen compounds. However, classical, nitrate-based fertilization is responsible for considerable environmental problems, such as the contamination of surface and underground water due to nitrate leaching, and the emission of greenhouse gases, owing to the effect of the micro-organisms in the soil that use the nitrate and produce nitrous oxide, a significant greenhouse gas. In order to alleviate these problems, "an attempt is being made to encourage a different type of fertilizer treatment, and one of them is the use of ammonia together with nitrification inhibitors. The inhibitors cause this ammonia to be in the soil for longer and this helps to mitigate nitrate leaching and also nitrous oxide emissions," explained Daniel Marino, researcher in the UPV/EHU's NUMAPS research group, which has conducted this study in collaboration with Dr Pedro Aparicio-Tejo of the UPN/NUP-Public University of Navarre. Yet this source of nitrogen has a special feature: "it can be toxic for plants and lead to reduced growth than when nitrate is used. In our group we are studying the tolerance and sensitivity of different plants to this source of nitrogen". Seeking to go further into this subject, they went on to study the proteome of a model plant, Arabidopsis thaliana. "Without focussing on any protein in particular, we decided to see what differences were displayed by this plant within the synthesised proteins as a whole when ammonium or nitric fertilizers are applied," said Daniel Marino. The same results in edible plants When studying the type and quantity of proteins accumulated in the plants with each type of nutrition, "what seemed most interesting to us is that there were some proteins related to the metabolism of glucosinolates which accumulate in a greater quantity in plants receiving an ammonium input," stressed the researcher. In general, glucosinolates have two properties: they are natural insecticides and one of them in particular, glucoraphanin, has anticarcinogenic properties. Given that the experiments had been conducted using the plant Arabidopsis thaliana, a model plant widely used in research but of no commercial interest, they decided to repeat the experiment, "but this time with broccoli plants. Although we did not manage to study the glucosinolate content in the part of the broccoli of greatest food interest, which is the flower, we saw that the leaves of the young plants accumulated a greater quantity of glucoraphanin when we added the source of nitrogen by means of ammonium than when we did so using nitrate," explained Marino. In view of these results, the research group is continuing to work on this aspect and they have even been in contact with several companies that could be interested in them. So in order to pursue their possible commercial application "we carried out field experiments where the system is much more complex, due, among other things, to the micro-organisms in the soil that also use ammonium as a source of nitrogen. So in the field experiments we will also be interested in analysing the glucosinolate content in the broccoli inflorescence, the part of the plant that is consumed most. On the other hand, from a more fundamental point of view, we are also interested in knowing the effect that the glucosinolates could have on the ammonium tolerance of the plant itself," he explained. The biologist Daniel Marino-Bilbao, an Ikerbasque Research Fellow at the UPV/EHU, is a member of the research group NUMAPS (Nutrition Management in Plant and Soil), led by Carmen González-Murua, of the department of Plant Biology and Ecology in the UPV/EHU's Faculty of Science and Technology. Marino D, Ariz I, Lasa B, Santamaría E, Fernández-Irigoyen J, González-Murua C, Aparicio-Tejo P (2016) Quantitative proteomics reveals the importance of nitrogen source to control glucosinolate metabolism in Arabidopsis thaliana and Brassica oleracea. Journal of Experimental Botany 67: 3313-3323.
Mateo-Alonso A.,University of the Basque Country |
Chemical Society Reviews | Year: 2014
Linear and ribbon-like polycyclic aromatic hydrocarbons such as acenes and graphene nanoribbons are at the forefront of current investigations, as these graphene "cut outs" possess discrete energy gaps that can be tailored with the number of rings and their arrangements. Pyrene-fused pyrazaacenes are a type of nitrogenated ribbon-like polycyclic aromatic hydrocarbons with a very high stability. As a matter of fact, ribbon-like pyrene-fused pyrazaacenes with as many as 85 linearly fused aromatic rings have been synthesised with thermal stabilities over 500 °C in air. This review covers most of the synthetic and application aspects of pyrene-fused pyrazaacenes from 1937 to our days, illustrating that pyrene-fused pyrazaacenes are a widely tuneable and a highly stable platform for developing ribbon-like nitrogenated polycyclic aromatic hydrocarbons for a broad spectrum of applications. © The Royal Society of Chemistry 2014.
Schive H.-Y.,National Taiwan University |
Chiueh T.,National Taiwan University |
Broadhurst T.,University of the Basque Country |
Nature Physics | Year: 2014
The conventional cold-particle interpretation of dark matter (known as 'cold dark matter', or CDM) still lacks laboratory support and struggles with the basic properties of common dwarf galaxies, which have surprisingly uniformcentralmasses and shallow density profiles1-5. In contrast, galaxies predicted by CDM extend to much lower masses, with steeper, singular profiles6-9. This tension motivates cold, wavelike dark matter ( DM) composed of a non-relativistic Bose-Einstein condensate, so the uncertainty principle counters gravity below a Jeans scale10-12. Here we achieve cosmological simulations of this quantum state at unprecedentedly high resolution capable of resolving dwarf galaxies, with only one free parameter, mB, the boson mass. We demonstrate the large-scale structure is indistinguishable from CDM, as desired, but diers radically inside galaxies where quantum interference forms solitonic cores surrounded by extended haloes of fluctuating density granules.These results allowus to determine m B=(8.0C+1.8 -2.0×10-23 eV using stellar phase-space distributions in dwarf spheroidal galaxies. Denser, more massive solitons are predicted for Milky Way sized galaxies, providing a substantial seed to help explain early spheroid formation. The onset of galaxy formation is substantially delayed relative to CDM, appearing at redshift z≲13 in our simulations. © 2014 Macmillan Publishers Limited. All rights reserved.
Marzari N.,Theory and Simulation of Materials THEOS |
Mostofi A.A.,Imperial College London |
Yates J.R.,University of Oxford |
Souza I.,University of the Basque Country |
And 2 more authors.
Reviews of Modern Physics | Year: 2012
The electronic ground state of a periodic system is usually described in terms of extended Bloch orbitals, but an alternative representation in terms of localized "Wannier functions" was introduced by Gregory Wannier in 1937. The connection between the Bloch and Wannier representations is realized by families of transformations in a continuous space of unitary matrices, carrying a large degree of arbitrariness. Since 1997, methods have been developed that allow one to iteratively transform the extended Bloch orbitals of a first-principles calculation into a unique set of maximally localized Wannier functions, accomplishing the solid-state equivalent of constructing localized molecular orbitals, or "Boys orbitals" as previously known from the chemistry literature. These developments are reviewed here, and a survey of the applications of these methods is presented. This latter includes a description of their use in analyzing the nature of chemical bonding, or as a local probe of phenomena related to electric polarization and orbital magnetization. Wannier interpolation schemes are also reviewed, by which quantities computed on a coarse reciprocal-space mesh can be used to interpolate onto much finer meshes at low cost, and applications in which Wannier functions are used as efficient basis functions are discussed. Finally the construction and use of Wannier functions outside the context of electronic-structure theory is presented, for cases that include phonon excitations, photonic crystals, and cold-atom optical lattices. © 2012 American Physical Society.
Grabowski Sl.J.,Donostia International Physics Center |
Physical Chemistry Chemical Physics | Year: 2014
MP2/aug-cc-pVTZ calculations were carried out on complexes of ZH 4, ZFH3 and ZF4 (Z = C, Si and Ge) molecules with HCN, LiCN and Cl- species acting as Lewis bases through nitrogen centre or chlorine ion. Z-Atoms in these complexes usually act as Lewis acid centres forming σ-hole bonds with Lewis bases. Such noncovalent interactions may adopt a name of tetrel bonds since they concern the elements of the group IV. There are exceptions for complexes of CH4 and CF 4, as well as for the F4Si⋯NCH complex where the tetrel bond is not formed. The energetic and geometrical parameters of the complexes were analyzed and numerous correlations between them were found. The Quantum Theory of 'Atoms in Molecules' and Natural Bonds Orbital (NBO) method used here should deepen the understanding of the nature of the tetrel bond. An analysis of the electrostatic potential surfaces of the interacting species is performed. The electron charge redistribution, being the result of the tetrel bond formation, is the same as that of the SN2 reaction. The energetic and geometrical parameters of the complexes analyzed here correspond to different stages of the SN2 process. This journal is © 2014 the Owner Societies.
Grabowski S.J.,Donostia International Physics Center |
Chemical Reviews | Year: 2011
Hydrogen bonding is an important interaction playing a key role in chemical, physical, and biochemical processes. The Quantum Theory of 'Atoms in Molecules' (QTAIM) is one of the approaches often applied to analyze the electron charge distribution for the hydrogen-bonded systems. The bond number connected with interatomic distance seems to be good to introduce a measure of strength for nonbonding contacts including hydrogen bonds. The bond number may be understood as the fraction of electron pair participating in the atom-atom contact, and the logarithmic relation is a consequence of the exponential character of intermolecular forces. The Natural Bond Orbital (NBO), also differ significantly from the other decomposition schemes. A measure of the hydrogen-bonding strength, named as a complex parameter, based on geometrical and topological parameters of the A-H proton-donating bond, was introduced and calculated for a sample of different hydrogen-bonded complexes.
Philosophical transactions of the Royal Society of London. Series B, Biological sciences | Year: 2014
As societal demand for food, water and other life-sustaining resources grows, the science of ecosystem services (ES) is seen as a promising tool to improve our understanding, and ultimately the management, of increasingly uncertain supplies of critical goods provided or supported by natural ecosystems. This promise, however, is tempered by a relatively primitive understanding of the complex systems supporting ES, which as a result are often quantified as static resources rather than as the dynamic expression of human-natural systems. This article attempts to pinpoint the minimum level of detail that ES science needs to achieve in order to usefully inform the debate on environmental securities, and discusses both the state of the art and recent methodological developments in ES in this light. We briefly review the field of ES accounting methods and list some desiderata that we deem necessary, reachable and relevant to address environmental securities through an improved science of ES. We then discuss a methodological innovation that, while only addressing these needs partially, can improve our understanding of ES dynamics in data-scarce situations. The methodology is illustrated and discussed through an application related to water security in the semi-arid landscape of the Great Ruaha river of Tanzania.
Agency: European Commission | Branch: FP7 | Program: MC-COFUND | Phase: FP7-PEOPLE-2013-COFUND | Award Amount: 15.63M | Year: 2014
The aim of this project is to reinforce the System of Science of the Basque Country, attracting excellence scientists from any country, in order to consolidate the Basque Region as a European Reference Point for excellence in research. Ikerbasque is a Foundation fostered by the Basque Government to strengthen the Basque Science System by means of attracting senior researchers. The new call, to be launched by Ikerbasque, will host incoming (non national and non resident researchers) and reintegrating (national and non resident) experienced researchers. The researchers must demonstrate their experience in, at least, one of the following research areas: Experimental sciences (Chemistry, Physic, Biology, Mathematics, Biophysics); Engineering and Technology (Chemical Engineer, Telecommunication, Industrial, Electrical and Electricity Engineer); Life Sciences (medicine); Social Sciences (economy, law, social psychology); Human Sciences (Psychology, Linguistics, History). The calls have regular selection rounds for experienced researchers based on an open and widely advertised competition, with transparent international peer review and selection of candidates based on their scientific excellence. The selection process assures no discrimination of researchers for any reason. The selected researchers will have a permanent contract and all the freedom to choose their own research programme, as well as the host institution amongst the universities, research centres and different laboratories that have an agreement with Ikerbasque. That research programme will fit his/her individual needs, providing the best conditions for his/her personal objectives and for the development of a valid research project. A special regard is given to working conditions and career development.
Agency: European Commission | Branch: FP7 | Program: MC-COFUND | Phase: FP7-PEOPLE-2012-COFUND | Award Amount: 16.73M | Year: 2013
The aim of this project is to reinforce the research potential of the European Research Area, and to consolidate the Basque Region as a Reference Point for excellence in research.Ikerbasque is a Foundation fostered by the Basque Government to strengthen the Basque Science System by means of attracting senior postdoctoral researchers. Ikerbasque currently manages two successful funding programmes running under the COFUND scheme, SmartBrain, offering full time positions for highly qualified and experienced researchers, and SmartFellows, providing short term sabbaticals for visiting researchers. In order to complement these two calls, Ikerbasque is implementing a novel complementary funding programme in the Basque Country for more junior postdoctoral positions to be supported for the next 5 years (from 2013 to 2018) through the current call of the Marie Curie COFUND programme. The new call to be launched on a yearly basis by Ikerbasque will host mainly incoming (non-national and non-resident researchers) postdoctoral researchers, and some reintegrating (national and non-resident) researchers will also be accepted if they comply with the eligibility criteria. The researchers can submit their applications in any research area. The selected researchers will have a temporary 5 year contract with all the freedom to choose their own research programme, as well as the host institution amongst the universities, research centres and different laboratories that have an agreement with Ikerbasque. They will be hosted in a research centre or university of their choice, where they will develop the research programme that best fits their individual needs, providing the best conditions for their personal objectives and for the development of a valid research project. Thus, WOLFRAM contributes to increase the research excellence in the private and/or the public sectors of the Scientific System of the Basque Country and, as a spin off effect, of the rest of the European Research Area.