New high-pressure phase and equation of state of Ce2Zr2O8

In this paper we report a new high-pressure rhombohedral phase of Ce2Zr2O8 observed from high-pressure angle-dispersive x-ray diffraction and Raman spectroscopy studies up to nearly 12 GPa. The ambient-pressure cubic phase of Ce2Zr2O8 transforms to a rhombohedral structure beyond 5 GPa with a feeble distortion in the lattice. Pressure evolution of unit-cell volume showed a change in compressibility above 5 GPa. The unit-cell parameters of the high-pressure rhombohedral phase at 12.1 GPa are ah = 14.6791(3) {\AA}, ch = 17.9421(5) {\AA}, V = 3348.1(1) {\AA}3. The structure relation between the parent cubic (P2_13) and rhombohedral (P3_2) phases were obtained by group-subgroup relations. All the Raman modes of the cubic phase showed linear evolution with pressure with the hardest one at 197 cm-1. Some Raman modes of the high-pressure phase have a non-linear evolution with pressure and softening of one low-frequency mode with pressure is found. The compressibility, equation of state, and pressure coefficients of Raman modes of Ce2Zr2O8 are also reported.Comment: 33 pages, 8 figures, 6 table

On the analysis of expected distance between sensor nodes and the base station in randomly deployed WSNs

In this study, we focus on the analytical derivation of the expected distance between all sensor nodes and the base station (i.e., E[dtoBS]) in a randomly deployed WSN. Although similar derivations appear in the related literature, to the best of our knowledge, our derivation, which assumes a particular scenario, has not been formulated before. In this specific scenario, the sensing field is a square-shaped region and the base station is located at some arbitrary distance to one of the edges of the square. Having the knowledge of E[dtoBS] value is important because E[dtoBS] provides a network designer with the opportunity to make a decision on whether it is energy-efficient to perform clustering for WSN applications that aim to pursue the clustered architectures. Similarly, a network designer might make use of this expected value during the process of deciding on the modes of communications (i.e., multi-hop or direct communication) after comparing it with the maximum transmission ranges of devices. Last but not least, the use of our derivation is not limited to WSN domain. It can be also exploited in any domain when there is a need for a probabilistic approach to find the average distance between any given number of points which are all assumed to be randomly and uniformly located in any square-shaped region and at a specific point outside this region. © Springer International Publishing Switzerland 2014

Sorting live stem cells based on Sox2 mRNA expression.

PMCID: PMC3507951This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.While cell sorting usually relies on cell-surface protein markers, molecular beacons (MBs) offer the potential to sort cells based on the presence of any expressed mRNA and in principle could be extremely useful to sort rare cell populations from primary isolates. We show here how stem cells can be purified from mixed cell populations by sorting based on MBs. Specifically, we designed molecular beacons targeting Sox2, a well-known stem cell marker for murine embryonic (mES) and neural stem cells (NSC). One of our designed molecular beacons displayed an increase in fluorescence compared to a nonspecific molecular beacon both in vitro and in vivo when tested in mES and NSCs. We sorted Sox2-MB(+)SSEA1(+) cells from a mixed population of 4-day retinoic acid-treated mES cells and effectively isolated live undifferentiated stem cells. Additionally, Sox2-MB(+) cells isolated from primary mouse brains were sorted and generated neurospheres with higher efficiency than Sox2-MB(-) cells. These results demonstrate the utility of MBs for stem cell sorting in an mRNA-specific manner

Experimental and theoretical investigations on structural and vibrational properties of melilite-type Sr2ZnGe2O7 at high pressure and delineation of a high pressure monoclinic phase

"This document is the Accepted Manuscript version of a Published Work that appeared in final form in Inorganic Chemistry, copyright © American Chemical Society after peer review and technical editing by the publisher. To access the final edited and published work see http://pubs.acs.org/doi/abs/10.1021/acs.inorgchem.5b00937"We report a combined experimental and theoretical study of melilite-type germanate, Sr2ZnGe2O7, under compression. In situ high-pressure X-ray diffraction and Raman scattering measurements up to 22 GPa were complemented with first-principles theoretical calculations of structural and lattice dynamics properties. Our experiments show that the tetragonal structure of Sr2ZnGe2O7 at ambient conditions transforms reversibly to a monoclinic phase above 12.2 Gpa with similar to 1% volume drop at the phase transition pressure. Density functional calculations indicate the transition pressure at, similar to 13 GPa, which agrees well with the experimental value. The structure of the high-pressure monoclinic phase is closely related to the ambient pressure phase and results from a displacive-type phase transition. Equations of state of both tetragonal and monoclinic phases are reported. Both of the phases show anisotropic compressibility with a larger compressibility in the direction perpendicular to the [ZnGe2O7](2-) sheets than along the sheets. Raman-active phonons of both the tetragonal and monoclinic phases and their pressure dependences were also determined. Tentative assignments of the Raman modes of the tetragonal phase were discussed in the light of lattice dynamics calculations. A possible irreversible second phase transition to a highly disordered or amorphous state is detected in Raman scattering measurements above 21 GPa.Research supported by the Spanish government MINECO under Grant Nos. MAT and CSD2007-00045 and MAT2013-46649-C4-1/2/3-P. S.N.A. acknowledges the support provided by Universitat de Valencia during his visit there.Achary, SN.; Errandonea, D.; Santamaría-Pérez, D.; Gomis, O.; Patwe, SJ.; Manjón Herrera, FJ.; Rodríguez Hernández, P.... (2015). Experimental and theoretical investigations on structural and vibrational properties of melilite-type Sr2ZnGe2O7 at high pressure and delineation of a high pressure monoclinic phase. Inorganic Chemistry. 54(13):6594-6605. doi:10.1021/acs.inorgchem.5b00937S65946605541

Exploring the high-pressure behavior of the three known polymorphs of BiPO4: Discovery of a new polymorph

The following article appeared in Journal of Applied Physics and may be found at http://dx.doi.org/10.1063/1.4914407 . Authors own version of final article on e-print serversWe have studied the structural behavior of bismuth phosphate under compression. We performed x-ray powder diffraction measurements up to 31.5 GPa and ab initio calculations. Experiments were carried out on different polymorphs: trigonal (phase I) and monoclinic (phases II and III). Phases I and III, at low pressure (P < 0.2-0.8 GPa), transform into phase II, which has a monazite-type structure. At room temperature, this polymorph is stable up to 31.5 GPa. Calculations support these findings and predict the occurrence of an additional transition from the monoclinic monazite-type to a tetragonal scheelite-type structure (phase IV). This transition was experimentally found after the simultaneous application of pressure (28 GPa) and temperature (1500 K), suggesting that at room temperature the transition might by hindered by kinetic barriers. Calculations also predict an additional phase transition at 52 GPa, which exceeds the maximum pressure achieved in the experiments. This transition is from phase IV to an orthorhombic barite-type structure (phase V). We also studied the axial and bulk compressibility of BiPO4. Room-temperature pressure-volume equations of state are reported. BiPO4 was found to be more compressible than isomorphic rare-earth phosphates. The discovered phase IV was determined to be the less compressible polymorph of BiPO4. On the other hand, the theoretically predicted phase V has a bulk modulus comparable with that of monazite-type BiPO4. Finally, the isothermal compressibility tensor for the monazite-type structure is reported at 2.4 GPa showing that the direction of maximum compressibility is in the (0 1 0) plane at approximately 15 degrees (21 degrees) to the a axis for the case of our experimental (theoretical) study. (C) 2015 AIP Publishing LLC.Research supported by the Spanish government MINECO under Grant No: MAT2013-46649-C4-1/2/3-P and by Generalitat Valenciana under Grants Nos. GVA-ACOMP-2013-1012 and GVA-ACOMP/2014/243. B.G.-D. thanks the financial support from MEC through FPI program. Experiments were performed at MSPD beamline at ALBA Synchrotron Light Facility with the collaboration of ALBA staff.Errandonea, D.; Gomis, O.; Santamaría Pérez, D.; García-Domene, B.; Muñoz, A.; Rodríguez-Hernández, P.; Achary, SN.... (2015). Exploring the high-pressure behavior of the three known polymorphs of BiPO4: Discovery of a new polymorph. Journal of Applied Physics. 117:105902-1-105902-9. https://doi.org/10.1063/1.4914407S105902-1105902-911

Mycobacterium tuberculosis ClpP Proteases Are Co-transcribed but Exhibit Different Substrate Specificities

PMCID: PMC3613350This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited

Genetic Resources of Pearl Millet: Status and Utilization

Pearl millet is a very important crop of arid and semi-arid regions in Asia and Africa where it is the basis of food security of millions of people inhabiting in harsh and environmentally fragile ecosystem. Genetic resources of pearl millet including landraces, improved elite material, traditional cultivars, genetic stocks and wild relatives are very rich and, therefore, their characterization, documentation, conservation and distribution is very essential to ensure utilization in breeding programmes. This review assesses the status of pearl millet genetic resources, and identifi es the gaps in their collection, conservation and utilization. A total of 56,580 accessions (including possible duplicates) of pearl millet in 70 genebanks of 46 countries across world are available. Landraces represent the largest part of pearl millet germplasm, followed by breeding/research material and wild relatives. The Indian national collection includes 7,059 accessions at the National Bureau of Plant Genetic Resources (NBPGR), New Delhi. Global collections managed by ICRISAT comprise of 22,888 pearl millet accessions from 51 countries. However, only a very small fraction of these accessions has been utilized so far. Critical assessment of collection for geographical and trait-diversity gaps using various GIS tools revealed several gaps in germplasm collection from Asian and African continents. Almost all cultivated accessions have been characterized for 23 morpho-agronomic characters following prescribed pearl millet descriptors. A large variation exists for phenotypic and phenological traits among available germplasm. In general, Indian pearl millet landraces have mainly contributed for earliness, high tillering, high harvest index and local adaptation; whereas African material has been a good source of bigger panicles, large seed size, and disease resistance. Systematic evaluation and screening of germplasm has led to the identifi cation of specifi c sources of better grain quality, resistance to diseases and tolerance to abiotic stresses like drought and heat. These germplasm sources continue to play a critical role in crop improvement programmes across the world. Formation of trait-specifi c gene pools, core and minicore collections are likely to enhance the utilization of genetic resources to a greater degree. Strategies for further enriching the germplasm and increasing its use are discussed

Specialized dynamical properties of promiscuous residues revealed by simulated conformational ensembles

The ability to interact with different partners is one of the most important features in proteins. Proteins that bind a large number of partners (hubs) have been often associated with intrinsic disorder. However, many examples exist of hubs with an ordered structure, and evidence of a general mechanism promoting promiscuity in ordered proteins is still elusive. An intriguing hypothesis is that promiscuous binding sites have specific dynamical properties, distinct from the rest of the interface and pre-existing in the protein isolated state. Here, we present the first comprehensive study of the intrinsic dynamics of promiscuous residues in a large protein data set. Different computational methods, from coarse-grained elastic models to geometry-based sampling methods and to full-atom Molecular Dynamics simulations, were used to generate conformational ensembles for the isolated proteins. The flexibility and dynamic correlations of interface residues with a different degree of binding promiscuity were calculated and compared considering side chain and backbone motions, the latter both on a local and on a global scale. The study revealed that (a) promiscuous residues tend to be more flexible than nonpromiscuous ones, (b) this additional flexibility has a higher degree of organization, and (c) evolutionary conservation and binding promiscuity have opposite effects on intrinsic dynamics. Findings on simulated ensembles were also validated on ensembles of experimental structures extracted from the Protein Data Bank (PDB). Additionally, the low occurrence of single nucleotide polymorphisms observed for promiscuous residues indicated a tendency to preserve binding diversity at these positions. A case study on two ubiquitin-like proteins exemplifies how binding promiscuity in evolutionary related proteins can be modulated by the fine-tuning of the interface dynamics. The interplay between promiscuity and flexibility highlighted here can inspire new directions in protein-protein interaction prediction and design methods. © 2013 American Chemical Society

High-pressure structural and vibrational properties of monazite-type BiPO4, LaPO4, CePO4, and PrPO4

[EN] Monazite-type BiPO4, LaPO4, CePO4, and PrPO4 have been studied under high pressure by ab initio simulations and Raman spectroscopy measurements in the pressure range of stability of the monazite structure. A good agreement between experimental and theoretical Raman-active mode frequencies and pressure coefficients has been found which has allowed us to discuss the nature of the Raman-active modes. Besides, calculations have provided us with information on how the crystal structure is modified by pressure. This information has allowed us to determine the equation of state and the isothermal compressibility tensor of the four studied compounds. In addition, the information obtained on the polyhedral compressibility has been used to explain the anisotropic axial compressibility and the bulk compressibility of monazite phosphates. Finally, we have carried out a systematic discussion on the high-pressure behavior of the four studied phosphates in comparison to results of previous studies.The authors are thankful for the financial support to this research from the Spanish Ministerio de Economia y Competitividad, the Spanish Research Agency, and the European Fund for Regional Development under Grant Nos: MAT2016-75586-C4-1-P/2-P/3-P and MAT2015-71070-REDC. AM and PR-H acknowledge computing time provided by Red Espanola de Supercomputacion (RES) and MALTA-Cluster.Errandonea, D.; Gomis, O.; Rodríguez Hernández, P.; Muñoz, A.; Ruiz Fuertes, J.; Gupta, M.; Achary, S.... (2018). High-pressure structural and vibrational properties of monazite-type BiPO4, LaPO4, CePO4, and PrPO4. Journal of Physics Condensed Matter. 30(6). https://doi.org/10.1088/1361-648X/aaa20dS30