Nanoporous Ge thin film production combining Ge sputtering and dopant implantation

International audienceIn this work a novel process allowing for the production of nanoporous Ge thin films is presented. This process uses the combination of two techniques: Ge sputtering on SiO 2 and dopant ion implantation. The process entails four successive steps: (i) Ge sputtering on SiO 2 , (ii) implantation preannealing, (iii) high-dose dopant implantation, and (iv) implantation postannealing. Scanning electron microscopy and transmission electron microscopy were used to characterize the morphology of the Ge film at different process steps under different postannealing conditions. For the same postannealing conditions, the Ge film topology was shown to be similar for different implantation doses and different dopants. However, the film topology can be controlled by adjusting the postannealing conditions

Toward the understanding of the brittle to ductile transition at low size in silicon: Experiments and simulations

While bulk silicon is brittle at temperatures below 600-700K, the compression of nanopillars has shown that a decrease of the diameter below few hundreds of nanometers could change the silicon behavior from brittle to ductile [1,2]. This size effect cannot be explained by the initial defect density like in metals, because pristine silicon nano-objects do not contain residual defects. In these conditions the cracks and/or the dislocations nucleation should take origin at the surface. The identification of the parameters governing the brittle to ductile transition in size and the understanding of the mechanisms are the key points to further develop the MEMS and NEMS technology or to prevent the failure of microelectronic components based on the silicon strained technology. Nowadays the respective improvements in simulations and experiments allow to investigate the mechanical properties of objects of similar sizes, close to hundreds of nanometers. We have then used both approaches - experiments and simulations – to understand the mechanisms at the origin of cracks and dislocations nucleation in such nanopillars. Experimentally,nanopillars with diameters of 100 nm and heights of 300 nm are obtained by lithography. They are deformed in compression by a flat punch nano-indentor under controlled-displacement mode at room temperature, and analyzed by scanning electron microscopy and high resolution transmission electron microscopy. In simulation, nanopillars up to 44 nm in diameter and height are investigated under compression and tension in controlled-displacement too, with a temperature ranging from 1 to 600K. The atomic interactions in silicon are modeled by two different semi-empirical potentials, Stillinger Weber and a Modified Embedded-Atom-Method (MEAM), both fitted to better reproduce the ductile and brittle properties of bulk silicon. Under compressive load (Fig. 1), both approaches reveal a ductile behavior with similar stress-strain curves, and large shear bands of amorphous silicon along the slip plane. In addition the simulations enlighten the formation of stacking fault plane in the anti-twining shear stress direction at the onset of plasticity, not yet confirmed by experiments (work in progress). The simulations under tensile load (Fig. 2) show the nucleation of perfect dislocations from the surface that can lead to cavity opening when they interact [3]. We observe first that the height of the nanopillars must be higher than 20 nm to allow the cavity opening, and second that the brittle to ductile transition is controlled by the diameter of the nanopillars, as observed experimentally in compression. The deformation of pillars with large diameters operates by cavity expansion leading to the brittle fracture, while pillars with smaller diameters are deformed by dislocations gliding leading to ductile fracture. Finally, the simulations in temperature seem to corroborate the fact that the size of the brittle to ductile transition could increase with temperature, as presumed experimentally [2]

The Molecular Biology Database Collection: 2008 update

The Nucleic Acids Research online Molecular Biology Database Collection is a public repository that lists more than 1000 databases described in this and previous Nucleic Acids Research annual database issues, as well as a selection of molecular biology databases described in other journals. All databases included in this Collection are freely available to the public. The 2008 update includes 1078 databases, 110 more than the previous one. The links to more than 80 databases have been updated and 25 obsolete databases have been removed from the list. The complete database list and summaries are available online at the Nucleic Acids Research web site, http://nar.oxfordjournals.org/

Next-generation sequencing of the chacma baboon and drill monkey cytomegalovirus genomes

Cynocephalus ursinus, Chacma Baboon, has natural and common infections of baboon cytomegalovirus (BaCMV). Mandrillus leucophaeus, Drill monkey, are an endangered species that also carries cytomegalovirus (DrCMV). Laboratories study the BaCMV and DrCMV as they share many features with human cytomegalovirus (HCMV) and thus is can be used as a model virus for HCMV research. Nonhuman primate cytomegalovirus is also studied to develop diagnostic assays to help primate colony health. With the introduction of next-generation sequencing we now have the capability of determining specific Chacma Baboon and Drill Monkey cytomegalovirus strain genomes in order to further this research

Lithic technological responses to Late Pleistocene glacial cycling at Pinnacle Point Site 5-6, South Africa

There are multiple hypotheses for human responses to glacial cycling in the Late Pleistocene, including changes in population size, interconnectedness, and mobility. Lithic technological analysis informs us of human responses to environmental change because lithic assemblage characteristics are a reflection of raw material transport, reduction, and discard behaviors that depend on hunter-gatherer social and economic decisions. Pinnacle Point Site 5-6 (PP5-6), Western Cape, South Africa is an ideal locality for examining the influence of glacial cycling on early modern human behaviors because it preserves a long sequence spanning marine isotope stages (MIS) 5, 4, and 3 and is associated with robust records of paleoenvironmental change. The analysis presented here addresses the question, what, if any, lithic assemblage traits at PP5-6 represent changing behavioral responses to the MIS 5-4-3 interglacial-glacial cycle? It statistically evaluates changes in 93 traits with no a priori assumptions about which traits may significantly associate with MIS. In contrast to other studies that claim that there is little relationship between broad-scale patterns of climate change and lithic technology, we identified the following characteristics that are associated with MIS 4: increased use of quartz, increased evidence for outcrop sources of quartzite and silcrete, increased evidence for earlier stages of reduction in silcrete, evidence for increased flaking efficiency in all raw material types, and changes in tool types and function for silcrete. Based on these results, we suggest that foragers responded to MIS 4 glacial environmental conditions at PP5-6 with increased population or group sizes, 'place provisioning', longer and/or more intense site occupations, and decreased residential mobility. Several other traits, including silcrete frequency, do not exhibit an association with MIS. Backed pieces, once they appear in the PP5-6 record during MIS 4, persist through MIS 3. Changing paleoenvironments explain some, but not all temporal technological variability at PP5-6.Social Science and Humanities Research Council of Canada; NORAM; American-Scandinavian Foundation; Fundacao para a Ciencia e Tecnologia [SFRH/BPD/73598/2010]; IGERT [DGE 0801634]; Hyde Family Foundations; Institute of Human Origins; National Science Foundation [BCS-9912465, BCS-0130713, BCS-0524087, BCS-1138073]; John Templeton Foundation to the Institute of Human Origins at Arizona State Universit

Kinetoplastid Phylogenomics Reveals the Evolutionary Innovations Associated with the Origins of Parasitism

The evolution of parasitism is a recurrent event in the history of life and a core problem in evolutionary biology. Trypanosomatids are important parasites and include the human pathogens Trypanosoma brucei, Trypanosoma cruzi, and Leishmania spp., which in humans cause African trypanosomiasis, Chagas disease, and leishmaniasis, respectively. Genome comparison between trypanosomatids reveals that these parasites have evolved specialized cell-surface protein families, overlaid on a well-conserved cell template. Understanding how these features evolved and which ones are specifically associated with parasitism requires comparison with related non-parasites. We have produced genome sequences for Bodo saltans, the closest known non-parasitic relative of trypanosomatids, and a second bodonid, Trypanoplasma borreli. Here we show how genomic reduction and innovation contributed to the character of trypanosomatid genomes. We show that gene loss has “streamlined” trypanosomatid genomes, particularly with respect to macromolecular degradation and ion transport, but consistent with a widespread loss of functional redundancy, while adaptive radiations of gene families involved in membrane function provide the principal innovations in trypanosomatid evolution. Gene gain and loss continued during trypanosomatid diversification, resulting in the asymmetric assortment of ancestral characters such as peptidases between Trypanosoma and Leishmania, genomic differences that were subsequently amplified by lineage-specific innovations after divergence. Finally, we show how species-specific, cell-surface gene families (DGF-1 and PSA) with no apparent structural similarity are independent derivations of a common ancestral form, which we call “bodonin.” This new evidence defines the parasitic innovations of trypanosomatid genomes, revealing how a free-living phagotroph became adapted to exploiting hostile host environments

Aptamers as theranostic agents: modifications, serum stability and functionalisation

Aptamers, and the selection process known as Systematic Evolution of Ligands by Exponential Enrichment (SELEX) used to generate them, were first described more than twenty years ago. Since then, there have been numerous modifications to the selectionprocedures. This review discusses the use of modified bases as a means of enhancing serum stability and producing effective therapeutic tools, as well as functionalising these nucleic acids to be used as potential diagnostic agents