A Hybrid model for the origin of photoluminescence from Ge nanocrystals in SiO2_2 matrix

In spite of several articles, the origin of visible luminescence from germanium nanocrystals in SiO$_2$ matrix is controversial even today. Some authors attribute the luminescence to quantum confinement of charge carriers in these nanocrystals. On the other hand, surface or defect states formed during the growth process, have also been proposed as the source of luminescence in this system. We have addressed this long standing query by simultaneous photoluminescence and Raman measurements on germanium nanocrystals embedded in SiO$_2$ matrix, grown by two different techniques: (i) low energy ion-implantation and (ii) atom beam sputtering. Along with our own experimental observations, we have summarized relevant information available in the literature and proposed a \emph{Hybrid Model} to explain the visible photoluminescence from nanocrystalline germanium in SiO$_2$ matrix.Comment: 23 pages, 8 figure

Response of mycorrhizal Touriga Nacional variety grapevines to high temperatures measured by calorespirometry and near-infrared spectroscopy

Heat stress negatively affects several physiological and biochemical processes in grapevine plants. In this work, two new methods, calorespirometry, which has been used to determine temperature adaptation in plants, and near-infrared (NIR) spectroscopy, which has been used to determine several grapevine-related traits and to discriminate among varieties, were tested to evaluate grapevine response to high temperatures. ‘Touriga Nacional’ variety grapevines, inoculated or not with Rhizoglomus irregulare or Funneliformis mosseae, were used in this study. Calorespirometric parameters and NIR spectra, as well as other parameters commonly used to assess heat injury in plants, were measured before and after high temperature exposure. Growth rate and substrate carbon conversion effciency, calculated from calorespirometric measurements, and stomatal conductance, were the most sensitive parameters for discriminating among high temperature responses of control and inoculated grapevines. The results revealed that, although this vine variety can adapt its physiology to temperatures up to 40 ºC, inoculation with R. irregulare could additionally help to sustain its growth, especially after heat shocks. Therefore, the combination of calorespirometry together with gas exchange measurements is a promising strategy for screening grapevine heat tolerance under controlled conditions and has high potential to be implemented in initial phases of plant breeding programsinfo:eu-repo/semantics/publishedVersio

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

Elastic properties of grafted microtubules

We use single-particle tracking to study the elastic properties of single microtubules grafted to a substrate. Thermal fluctuations of the free microtubule's end are recorded, in order to measure position distribution functions from which we calculate the persistence length of microtubules with contour lengths between 2.6 and 48 micrometers. We find the persistence length to vary by more than a factor of 20 over the total range of contour lengths. Our results support the hypothesis that shearing between protofilaments contributes significantly to the mechanics of microtubules.Comment: 9 pages, 3 figure

Mammalian Adaptation of an Avian Influenza A Virus Involves Stepwise Changes in NS1

Influenza A viruses (IAVs) are common pathogens of birds that occasionally establish endemic infections in mammals. The processes and mechanisms that result in IAV mammalian adaptation are poorly understood. The viral non-structural 1 (NS1) protein counteracts the interferon (IFN) response, a central component of the host-species barrier. We characterised the NS1 proteins of equine influenza virus (EIV), a mammalian IAV lineage of avian origin. We showed that evolutionary distinct NS1s counteract the IFN response using different and mutually exclusive mechanisms: while the NS1s of early EIVs block general gene expression by binding to the cellular polyadenylation specific factor 30 (CPSF30), NS1s from more evolved EIVs specifically block the induction of IFN-stimulated genes by interfering with the JAK/STAT pathway. These contrasting anti-IFN strategies are associated with two mutations that appeared sequentially and became rapidly selected during EIV evolution, highlighting the importance of evolutionary processes on immune evasion mechanisms during IAV adaptation

Functional significance may underlie the taxonomic utility of single amino acid substitutions in conserved proteins

We hypothesized that some amino acid substitutions in conserved proteins that are strongly fixed by critical functional roles would show lineage-specific distributions. As an example of an archetypal conserved eukaryotic protein we considered the active site of ß-tubulin. Our analysis identified one amino acid substitution—ß-tubulin F224—which was highly lineage specific. Investigation of ß-tubulin for other phylogenetically restricted amino acids identified several with apparent specificity for well-defined phylogenetic groups. Intriguingly, none showed specificity for “supergroups” other than the unikonts. To understand why, we analysed the ß-tubulin Neighbor-Net and demonstrated a fundamental division between core ß-tubulins (plant-like) and divergent ß-tubulins (animal and fungal). F224 was almost completely restricted to the core ß-tubulins, while divergent ß-tubulins possessed Y224. Thus, our specific example offers insight into the restrictions associated with the co-evolution of ß-tubulin during the radiation of eukaryotes, underlining a fundamental dichotomy between F-type, core ß-tubulins and Y-type, divergent ß-tubulins. More broadly our study provides proof of principle for the taxonomic utility of critical amino acids in the active sites of conserved proteins

Rhesus TRIM5α disrupts the HIV-1 capsid at the inter-hexamer interfaces

TRIM proteins play important roles in the innate immune defense against retroviral infection, including human immunodeficiency virus type-1 (HIV-1). Rhesus macaque TRIM5α (TRIM5αrh) targets the HIV-1 capsid and blocks infection at an early post-entry stage, prior to reverse transcription. Studies have shown that binding of TRIM5α to the assembled capsid is essential for restriction and requires the coiled-coil and B30.2/SPRY domains, but the molecular mechanism of restriction is not fully understood. In this study, we investigated, by cryoEM combined with mutagenesis and chemical cross-linking, the direct interactions between HIV-1 capsid protein (CA) assemblies and purified TRIM5αrh containing coiled-coil and SPRY domains (CC-SPRYrh). Concentration-dependent binding of CC-SPRYrh to CA assemblies was observed, while under equivalent conditions the human protein did not bind. Importantly, CC-SPRYrh, but not its human counterpart, disrupted CA tubes in a non-random fashion, releasing fragments of protofilaments consisting of CA hexamers without dissociation into monomers. Furthermore, such structural destruction was prevented by inter-hexamer crosslinking using P207C/T216C mutant CA with disulfide bonds at the CTD-CTD trimer interface of capsid assemblies, but not by intra-hexamer crosslinking via A14C/E45C at the NTD-NTD interface. The same disruption effect by TRIM5αrh on the inter-hexamer interfaces also occurred with purified intact HIV-1 cores. These results provide insights concerning how TRIM5α disrupts the virion core and demonstrate that structural damage of the viral capsid by TRIM5α is likely one of the important components of the mechanism of TRIM5α-mediated HIV-1 restriction. © 2011 Zhao et al

Computationally efficient flux variability analysis

<p>Abstract</p> <p>Background</p> <p>Flux variability analysis is often used to determine robustness of metabolic models in various simulation conditions. However, its use has been somehow limited by the long computation time compared to other constraint-based modeling methods.</p> <p>Results</p> <p>We present an open source implementation of flux variability analysis called fastFVA. This efficient implementation makes large-scale flux variability analysis feasible and tractable allowing more complex biological questions regarding network flexibility and robustness to be addressed.</p> <p>Conclusions</p> <p>Networks involving thousands of biochemical reactions can be analyzed within seconds, greatly expanding the utility of flux variability analysis in systems biology.</p

Novel Materials, Processing and Device Technologies for Space Exploration with Potential Dual-Use Applications

We highlight results of a broad spectrum of efforts on lower-temperature processing of nanomaterials, novel approaches to energy conversion, and environmentally rugged devices. Solution-processed quantum dots of copper indium chalcogenide semiconductors and multiwalled carbon nanotubes from lower-temperature spray pyrolysis are enabled by novel (precursor) chemistry. Metal-doped zinc oxide (ZnO) nanostructured components of photovoltaic cells have been grown in solution at low temperature on a conductive indium tin oxide substrate. Arrays of ZnO nanorods can be templated and decorated with various semiconductor and metallic nanoparticles. Utilizing ZnO in a more broadly defined energy conversion sense as photocatalysts, unwanted organic waste materials can potentially be repurposed. Current efforts on charge carrier dynamics in nanoscale electrode architectures used in photoelectrochemical cells for generating solar electricity and fuels are described. The objective is to develop oxide nanowire-based electrode architectures that exhibit improved charge separation, charge collection and allow for efficient light absorption. Investigation of the charge carrier transport and recombination properties of the electrodes will aid in the understanding of how nanowire architectures improve performance of electrodes for dye-sensitized solar cells. Nanomaterials can be incorporated in a number of advanced higher-performance (i.e. mass specific power) photovoltaic arrays. Advanced technologies for the deposition of 4H-silicon carbide are described. The use of novel precursors, advanced processing, and process studies, including modeling are discussed from the perspective of enhancing the performance of this promising material for enabling technologies such as solar electric propulsion. Potential impact(s) of these technologies for a variety of aerospace applications are highlighted throughout. Finally, examples are given of technologies with potential spin-offs for dual-use or terrestrial applications