Combined use of 16S ribosomal DNA and 16S rRNA to study the bacterial community of polychlorinated biphenyl-polluted soil

The bacterial diversity assessed from clone libraries prepared from rRNA (two libraries) and ribosomal DNA (rDNA) (one library) from polychlorinated biphenyl (PCB)-polluted soil has been analyzed. A good correspondence of the community composition found in the two types of library was observed. Nearly 29% of the cloned sequences in the rDNA library were identical to sequences in the rRNA libraries. More than 60% of the total cloned sequence types analyzed were grouped in phylogenetic groups (a clone group with sequence similarity higher than 97% [98% for Burkholderia andPseudomonas-type clones]) represented in both types of libraries. Some of those phylogenetic groups, mostly represented by a single (or pair) of cloned sequence type(s), were observed in only one of the types of library. An important difference between the libraries was the lack of clones representative of the Actinobacteriain the rDNA library. The PCB-polluted soil exhibited a high bacterial diversity which included representatives of two novel lineages. The apparent abundance of bacteria affiliated to the beta-subclass of theProteobacteria, and to the genus Burkholderiain particular, was confirmed by fluorescence in situ hybridization analysis. The possible influence on apparent diversity of low template concentrations was assessed by dilution of the RNA template prior to amplification by reverse transcription-PCR. Although differences in the composition of the two rRNA libraries obtained from high and low RNA concentrations were observed, the main components of the bacterial community were represented in both libraries, and therefore their detection was not compromised by the lower concentrations of template used in this study

Site multiplicity of rare earth ions in III-nitrides

This presentation reviews recent lattice location studies of RE ions in GaN by electron emission channelling (EC) and X-ray absorption fine structure (XAFS) techniques. These studies agree that RE ions at low concentrations (whether they are incorporated during growth or introduced later by ion implantation) predominantly occupy Ga substitutional sites, as expected from considerations of charge equivalence. We combine this result with some examples of the welldocumented richness of optical spectra of GaN:RE3+ to suggest that the luminescence of these materials may be ascribed to a family of rather similar sites, all of which feature the REGa defect

Microtubules in Bacteria: Ancient Tubulins Build a Five-Protofilament Homolog of the Eukaryotic Cytoskeleton

Microtubules play crucial roles in cytokinesis, transport, and motility, and are therefore superb targets for anti-cancer drugs. All tubulins evolved from a common ancestor they share with the distantly related bacterial cell division protein FtsZ, but while eukaryotic tubulins evolved into highly conserved microtubule-forming heterodimers, bacterial FtsZ presumably continued to function as single homopolymeric protofilaments as it does today. Microtubules have not previously been found in bacteria, and we lack insight into their evolution from the tubulin/FtsZ ancestor. Using electron cryomicroscopy, here we show that the tubulin homologs BtubA and BtubB form microtubules in bacteria and suggest these be referred to as “bacterial microtubules” (bMTs). bMTs share important features with their eukaryotic counterparts, such as straight protofilaments and similar protofilament interactions. bMTs are composed of only five protofilaments, however, instead of the 13 typical in eukaryotes. These and other results suggest that rather than being derived from modern eukaryotic tubulin, BtubA and BtubB arose from early tubulin intermediates that formed small microtubules. Since we show that bacterial microtubules can be produced in abundance in vitro without chaperones, they should be useful tools for tubulin research and drug screening

Optical energies of AllnN epilayers

Optical energy gaps are measured for high-quality Al1−xInxN-on-GaN epilayers with a range of compositions around the lattice match point using photoluminescence and photoluminescence excitation spectroscopy. These data are combined with structural data to determine the compositional dependence of emission and absorption energies. The trend indicates a very large bowing parameter of 6 eV and differences with earlier reports are discussed. Very large Stokes' shifts of 0.4-0.8 eV are observed in the composition range 0.13<x<0.24, increasing approximately linearly with InN fraction despite the change of sign of the piezoelectric fiel

Size-selective breaking of the core-shell structure of gallium nanoparticles

This Accepted Manuscript is available for reuse under a CC BY-NC-ND 3.0 licence after the 12 month embargo period provided that all the terms of the licence are adhered toCore-shell gallium nanoparticles (Ga NPs) have recently been proposed as an ultraviolet plasmonic material for different applications but only at room temperature. Here, the thermal stability as a function of the size of the NPs is reported over a wide range of temperatures. We analyze the chemical and structural properties of the oxide shell by x-ray photoelectron spectroscopy and atomic force microscopy. We demonstrate the inverse dependence of the shell breaking temperature with the size of the NPs. Spectroscopic ellipsometry is used for tracking the rupture and its mechanism is systematically investigated by scanning electron microscopy, grazing incidence x-ray diffraction and cathodoluminescence. Taking advantage of the thermal stability of the NPs, we perform complete oxidations that lead to homogenous gallium oxide NPs. Thus, this study set the physical limits of Ga NPs to last at high temperatures, and opens up the possibility to achieve totally oxidized NPs while keeping their sphericityThe research is supported by the MINECO (CTQ2014-53334-C2-2-R, CTQ2017-84309-C2-2-R, MAT2016-80394-R, MAT 2015-65274-R/FEDER and MAT2017-85089-C2-1-R) and Comunidad de Madrid (NANOAVANSENS ref. S2013/MIT-3029) projects. ARC acknowledges Ramón y Cajal program (under contract number RYC-2015-18047). FN acknowledges support from Marie Sklodowska-Curie grant agreement No. 641899 from the European Union´s Horizon 2020 research and innovation programm

Instability of cosmological event horizons of non-static global cosmic strings

The stability of the cosmological event horizons found recently by Gregory [Phys. Rev. D54, 4955 (1996)] for a class of non-static global cosmic strings is studied. It is shown that they are not stable to both test particles and physical perturbations. In particular, the back reaction of the perturbations of null dust fluids will turn them into spacetime singularities. The resulted singularities are strong in the sense that the distortion of test particles diverges logarithmically when these singular hypersurfaces are approaching.Comment: Latex, no figure

Combining VIVO and Google Scholar data as sources for CERIF linked data: a case in the agricultural domain

The needs of global science have fostered open access to the results and contextual information of research organizations at an international scale. This requires the use of standards or shared data models to exchange information preserving its semantics when transferred between systems. In that direction, standards as CERIF or projects as VIVO were developed to exchange or expose the scientific knowledge. Also, there are other sources of scientific information in the Web that are useful to complement institutional repositories and CRISes. The heterogeneity of data models behind each source in turn raises the need for mappings between them to ease interchange and aggregate information. In this paper, we present a tool that integrates three sources of research information and enables their aggregating and export into both VIVO and CERIF models. We present a case study in agriculture using OpenAGRIS, a bibliographic database linked to Web sources with more than 7 million records. Concretely, we describe the methods to combine Google Scholar data for the scholarly content indexed in OpenAGRIS and aggregating new information provided by the first one, using our tool. Finally the information is stored in a VIVO instance and then translated into CERIF using a conversion process mapping both data models. The case demonstrates the possibilities of mapping tools to aggregate and translate CRIS information

Ectopic A-lattice seams destabilize microtubules

Natural microtubules typically include one A-lattice seam within an otherwise helically symmetric B-lattice tube. It is currently unclear how A-lattice seams influence microtubule dynamic instability. Here we find that including extra A-lattice seams in GMPCPP microtubules, structural analogues of the GTP caps of dynamic microtubules, destabilizes them, enhancing their median shrinkage rate by >20-fold. Dynamic microtubules nucleated by seeds containing extra A-lattice seams have growth rates similar to microtubules nucleated by B-lattice seeds, yet have increased catastrophe frequencies at both ends. Furthermore, binding B-lattice GDP microtubules to a rigor kinesin surface stabilizes them against shrinkage, whereas microtubules with extra A-lattice seams are stabilized only slightly. Our data suggest that introducing extra A-lattice seams into dynamic microtubules destabilizes them by destabilizing their GTP caps. On this basis, we propose that the single A-lattice seam of natural B-lattice MTs may act as a trigger point, and potentially a regulation point, for catastrophe

Nanomechanics of microtubules

We have determined the mechanical anisotropy of a single microtubule by simultaneously measuring the Young's and the shear moduli in vitro. This was achieved by elastically deforming the microtubule deposited on a substrate tailored by electron-beam lithography with a tip of an atomic force microscope. The shear modulus is 2 orders of magnitude lower than the Young's, giving rise to a length-dependent flexural rigidity of microtubules. The temperature dependence of the microtubule's bending stiffness in the (5-40) degreesC range shows a strong variation upon cooling coming from the increasing interaction between the protofilaments

Structural insights into RNA processing by the human RISC-loading complex.

Targeted gene silencing by RNA interference (RNAi) requires loading of a short guide RNA (small interfering RNA (siRNA) or microRNA (miRNA)) onto an Argonaute protein to form the functional center of an RNA-induced silencing complex (RISC). In humans, Argonaute2 (AGO2) assembles with the guide RNA-generating enzyme Dicer and the RNA-binding protein TRBP to form a RISC-loading complex (RLC), which is necessary for efficient transfer of nascent siRNAs and miRNAs from Dicer to AGO2. Here, using single-particle EM analysis, we show that human Dicer has an L-shaped structure. The RLC Dicer's N-terminal DExH/D domain, located in a short 'base branch', interacts with TRBP, whereas its C-terminal catalytic domains in the main body are proximal to AGO2. A model generated by docking the available atomic structures of Dicer and Argonaute homologs into the RLC reconstruction suggests a mechanism for siRNA transfer from Dicer to AGO2