Irradiation-induced defects in different glasses demonstrated on a metaphosphate glass

The influence of the two polyvalent ions, cobalt and nickel, on the formation of irradiation-induced defects was studied in several different model glasses (silicate, borosilicate, fluoride- and phosphate glasses). In this article the defects are demonstrated on the example of the (SrPO3)2-metaphosphate glass P100. Sample plates of high-purity glasses, undoped and doped with 0.3 mol% CoO and NiO, were irradiated with a UV lamp and with X-rays. The subsequent defect centers, formed at ppm levels, were characterized by EPR as well as optical UV-VIS spectroscopy. Defect recovery experiments were also studied in these glasses. The newly found optical bands and EPR signals evolving in the irradiated glass are in part characteristic for intrinsic defects. These are different types of electron centers (EC) and hole centers (HC) connected with phosphate groups. Other signals arise from extrinsic defects, which are caused by the two dopant ions. The predominant extrinsic defect stems from the photooxidation of Co2+ to (Co2+)2. As an HC the latter replaces some of the intrinsie phosphate-bonded HC and dominates the optical spectra with two bands at 300 and 400 nm. In the glass P100 lamp irradiation photoionizes only Co2+ but not Ni2+. Α new optical band at 330 nm, as well as a new EPR signal at g = 2.08 can be seen only after X-ray irradiadon. Both can be attributed to a nickel-related EC created via the photoreduction of Ni2+ to (Ni2+)-. At the same time the band of the intrinsic oxygen-related HC is intensified. Generally X-ray irradiation causes stronger irradiation-induced defects (excitation of inner electrons) than UV-lamp irradiation (selective excitation of valence electrons)

Influence of melting and annealing conditions on the optical spectra of a borosilicate glass doped with CoO and NiO

In the high-viscosity borosilicate glass (NBS2) doped with 0.3 mol% CoO or NiO quenching resulted in a freeze-in snap-shot of the glass structure within the dopants' transformation process from their high-temperature tetrahedral coordination to the octahedral form normally present in this glass at room temperature. In this transitional state the octahedral, tetrahedral and a third pseudotetrahedral transitional coordination are simultaneously present. The optical spectra of the doped glasses are discussed in relation to the different melting and cooling conditions applied. Quenched glasses were also tempered on a heating table, which permitted to take the optical spectra at each temperature step. In contrast to Co2+, Ni2+ has a strong octahedral preference. Thus for NiO-doped NBS2 glass tempering or annealing always results in relaxation into the octahedral coordination. For Co2+, which is also octahedrally coordinated in the annealed NBS2, tempering of the quenched glass leads to a relaxation into octahedrally and tetrahedrally coordinated Co2+. These structural changes are especially strong when the applied temperatures lie 150 to 200 °C above Tg of the NBS2 glass where also the viscosity-temperature curve implies structural changes within the glass matrix

UV light induced photoreduction in phosphate and fluoridephosphate glasses doped with Ni2+, Ta5+, Pb2+, and Ag+ compounds

The photoreduction of polyvalent ions was studied in high purity fluoride-phosphate and metaphosphate glasses doped with Ni2+ (3d8), Ta5+ (5d0), Pb2+ (6d2), and Ag+ (3d10). Compared to the undoped base glasses all doped samples display different electronic transitions in the UV at the irradiation wavelength. Glass samples containing 50 to 5000 ppm dopants were irradiated with excimer lasers at 193 and 248 nm, respectively. The subsequent defect centers, formed at ppm levels, were characterized by EPR and optical UV-VIS spectroscopy. The observed laser induced transmission losses in the UV and visible range increased in the order Ni, Ta, Pb to Ag. Extrinsic electron centers are formed by photoreduction of the dopants. (Ni2+)- is characterized by an optical transition with a maximum at 355 nm and an EPR signal around g ≈ 2.07. The maxima of the optical transitions of the (Pb2+)- -EC are positioned at 395 and 500 nm, of the (Ta5+)- -EC at 465 nm. The photoionization products of silver depend strongly on the silver concentration. At a silver content of 50 ppm only the (Ag+)- -EC is formed, visible in the optical spectra with a maximum around 450 nm. Α second silver species, (Ag+)2 -, which absorbs at 305 nm, is additionally observed in the sample doped with a silver concentration of 500 ppm. In the sample doped with 5000 ppm silver a third defect, the photooxidized (Ag+)+ -HC, with an optical band maximum at 405 nm and an EPR signal around g ≈ 2.3 is observed as well. The formation of extrinsic electron centers causes in all glasses an increase in the formation of intrinsic hole centers and often a decrease in the formation of intrinsic electron centers. Defect generation curves show that a very rapid darkening in the glasses is initiated by the addition of any of these dopants. The recovery rates of the defeets formed depend strongly on the dopant, not on the glass matrix

Plasticity, crack initiation and defect resistance in alkali-borosilicate glasses: From normal to anomalous behavior

We provide a comprehensive description of the defect tolerance of sodium-borosilicate glasses upon sharp contact loading. This is motivated by the key role which is taken by this particular glass system in a wide variety of applications, ranging from electronic substrates, display covers and substrates for biomedical imaging and sensing to, e.g., radioactive waste vitrification. The present report covers the mechanical properties of glasses in the Na2O–B2O3–SiO2 ternary over the broad range of compositions from pure SiO2 to binary sodium-borates, and crossing the regions of various commercially relevant specialty borosilicate glasses, such as the multi-component Duran-, Pyrex- and BK7-type compositions and typical soda-lime silicate glasses, which are also included in this study. In terms of structure, the considered glasses may be separated into two groups, that is, one series which contains only bridging oxygen atoms, and another series which is designed with an increasing number of non-bridging oxygen ions. Elastic moduli, Poisson ratio, hardness as well as creep and crack resistance were evaluated, as well as the contribution of densification to the overall amount of indentation deformation. Correlations between the mechanical properties and structural characteristics of near- and mid-range order are discussed, from which we obtain a mechanistic view at the molecular reactions which govern the overall deformation reaction and, ultimately, contact cracking

Microcompression experiments on glasses ‐ strain rate sensitive cracking behavior

Figure 11 – microcompression experiments on glasses showing stable crack growth (a) and reversible deformation (b) It is well known that the mechanical properties of glasses are closely related to their atomic structure. The exact structure-property-relationship, however, is only poorly understood even for fundamental mechanisms like shear and densification. Nanomechanical test methods like micropillar compression and nano indentation can help fill this gap. In this study a sodium-boro-silicate glass is quenched from different temperatures to induce changes in the atomic structure. Micropillar compression was used to introduce plastic deformation into these glasses at room temperature under a uniaxial stress state. By changing the strain rate it is shown that deformation shifts from completely reversible deformation, to stable crack growth, and finally brittle failure. It is shown that by changing the glass structure, the strain rates corresponding to these deformation regimes are shifted. Finally, the occurrence of shear and densification is discussed. These findings are analysed against the background of the glass structure. Please click Additional Files below to see the full abstract

Using impact‐nanoindentation to test glasses at high strain rates and room temperature

In many daily applications glasses are indispensable, and novel applications demanding improved strength and crack resistance are appearing continuously. Up to now, the fundamental mechanical processes in glasses subjected to high strain rates at room temperature are largely unknown and thus guidelines for one of the major failure conditions of glass components are non-existent. Here, we elucidate this important regime for the first time using glasses ranging from a dense metallic glass to open fused silica by impact as well as quasi-static nano-indentation. We show that towards high strain rates, shear deformation becomes the dominant mechanism in all glasses accompanied by Non-Newtonian behavior evident in a drop of viscosity with increasing rate covering eight orders of magnitude. All glasses converge to the same limit stress determined by the theoretical hardness, thus giving the first experimental and quantitative evidence that Non-Newtonian shear flow occurs at the theoretical strength at room temperature

Type III restriction endonuclease EcoP15I is a heterotrimeric complex containing one Res subunit with several DNA-binding regions and ATPase activity

For efficient DNA cleavage, the Type III restriction endonuclease EcoP15I communicates with two inversely oriented recognition sites in an ATP-dependent process. EcoP15I consists of methylation (Mod) and restriction (Res) subunits forming a multifunctional enzyme complex able to methylate or to cleave DNA. In this study, we determined by different analytical methods that EcoP15I contains a single Res subunit in a Mod2Res stoichiometry. The Res subunit comprises a translocase (Tr) domain carrying functional motifs of superfamily 2 helicases and an endonuclease domain with a PD..D/EXK motif. We show that the isolated Tr domain retains ATP-hydrolyzing activity and binds single- and double-stranded DNA in a sequence-independent manner. To localize the regions of DNA binding, we screened peptide arrays representing the entire Res sequence for their ability to interact with DNA. We discovered four DNA-binding regions in the Tr domain and two DNA-binding regions in the endonuclease domain. Modelling of the Tr domain shows that these multiple DNA-binding regions are located on the surface, free to interact with DNA. Interestingly, the positions of the DNA-binding regions are conserved among other Type III restriction endonucleases

Ion conducting and paramagnetic d-PCL(530)/siloxane-based biohybrids doped with Mn 2+ ions

Amorphous α,ω-hidroxylpoly(ε-caprolactone) (PCL(530))/siloxane ormolytes doped with manganese perchlorate (Mn(ClO4)2) (d-PCL(530)/siloxanenMn(ClO4)2) with n = 20, 50, and 100), thermally stable up to at least 200 ºC, were synthesized by the sol-gel method. Ionic conductivity values up to 4.8×10−8 and 2.0×10−6 S cm−1 at about 25 and 100 ºC, respectively, where obtained for n = 20. FT-IR data demonstrated that the hydrogen bonding interactions present in the non-doped d-PCL(530)/siloxane host hybrid matrix were significantly influenced by the inclusion of Mn(ClO4)2 which promoted the formation of more oxyethylene/urethane and urethane/urethane aggregates. In addition, the Mn2+ ions bonded to all the “free” C=O groups of the urethane cross-links and to some of the “free” ester groups of the amorphous PCL(530) chains. In the electrolytes, the ClO4 − ions were found “free” and bonded to the Mn2+ ions along a bidentate configuration. The magnitude of the electron paramagnetic resonance (EPR) hyperfine constant of the analyzed samples (A ≈ 90×10-4 cm−1 ) suggested that the bonding between Mn2+ ions and the surrounding ligands is moderately ionic. The synthetized d-PCL(530)/siloxanenMn(ClO4)2 biohybrids have potential application in paramagnetic, photoelectrochemical and electrochromic devices.This work was supported by Fundacao para a Ciencia e a Tecnologia (FCT) and Feder (contracts PTDC/CTM-BPC/112774/2009, PEst-OE/QUI/UI0616/2014 and PEst-C/QUI/UI0686/2013) and COST Action MP1202 "Rational design of hybrid organic-inorganic interfaces". R.F.P.P. acknowledges FCT for a grant (SFRH/BPD/87759/2012). M.M.S. acknowledges CNPq (PVE grant 406617/2013-9), for a mobility grant. The financial support of the Brazilian agencies Capes and CNPq are gratefully acknowledged. Research was partially financed by the CeRTEV, Center for Research, Technology and Education in Vitreous Materials, FAPESP 2013/07793-6.info:eu-repo/semantics/publishedVersio

SARS-CoV-2 variant Alpha has a spike-dependent replication advantage over the ancestral B.1 strain in human cells with low ACE2 expression

Epidemiological data demonstrate that Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) variants of concern (VOCs) Alpha and Delta are more transmissible, infectious, and pathogenic than previous variants. Phenotypic properties of VOC remain understudied. Here, we provide an extensive functional study of VOC Alpha replication and cell entry phenotypes assisted by reverse genetics, mutational mapping of spike in lentiviral pseudotypes, viral and cellular gene expression studies, and infectivity stability assays in an enhanced range of cell and epithelial culture models. In almost all models, VOC Alpha spread less or equally efficiently as ancestral (B.1) SARS-CoV-2. B.1. and VOC Alpha shared similar susceptibility to serum neutralization. Despite increased relative abundance of specific sgRNAs in the context of VOC Alpha infection, immune gene expression in infected cells did not differ between VOC Alpha and B.1. However, inferior spreading and entry efficiencies of VOC Alpha corresponded to lower abundance of proteolytically cleaved spike products presumably linked to the T716I mutation. In addition, we identified a bronchial cell line, NCI-H1299, which supported 24-fold increased growth of VOC Alpha and is to our knowledge the only cell line to recapitulate the fitness advantage of VOC Alpha compared to B.1. Interestingly, also VOC Delta showed a strong (595-fold) fitness advantage over B.1 in these cells. Comparative analysis of chimeric viruses expressing VOC Alpha spike in the backbone of B.1, and vice versa, showed that the specific replication phenotype of VOC Alpha in NCI-H1299 cells is largely determined by its spike protein. Despite undetectable ACE2 protein expression in NCI-H1299 cells, CRISPR/Cas9 knock-out and antibody-mediated blocking experiments revealed that multicycle spread of B.1 and VOC Alpha required ACE2 expression. Interestingly, entry of VOC Alpha, as opposed to B.1 virions, was largely unaffected by treatment with exogenous trypsin or saliva prior to infection, suggesting enhanced resistance of VOC Alpha spike to premature proteolytic cleavage in the extracellular environment of the human respiratory tract. This property may result in delayed degradation of VOC Alpha particle infectivity in conditions typical of mucosal fluids of the upper respiratory tract that may be recapitulated in NCI-H1299 cells closer than in highly ACE2-expressing cell lines and models. Our study highlights the importance of cell model evaluation and comparison for in-depth characterization of virus variant-specific phenotypes and uncovers a fine-tuned interrelationship between VOC Alpha- and host cell-specific determinants that may underlie the increased and prolonged virus shedding detected in patients infected with VOC Alpha

Type III restriction-modification enzymes: a historical perspective

Restriction endonucleases interact with DNA at specific sites leading to cleavage of DNA. Bacterial DNA is protected from restriction endonuclease cleavage by modifying the DNA using a DNA methyltransferase. Based on their molecular structure, sequence recognition, cleavage position and cofactor requirements, restriction-modification (R-M) systems are classified into four groups. Type III R-M enzymes need to interact with two separate unmethylated DNA sequences in inversely repeated head-to-head orientations for efficient cleavage to occur at a defined location (25-27 bp downstream of one of the recognition sites). Like the Type I R-M enzymes, Type III R-M enzymes possess a sequence-specific ATPase activity for DNA cleavage. ATP hydrolysis is required for the long-distance communication between the sites before cleavage. Different models, based on 1D diffusion and/or 3D-DNA looping, exist to explain how the long-distance interaction between the two recognition sites takes place. Type III R-M systems are found in most sequenced bacteria. Genome sequencing of many pathogenic bacteria also shows the presence of a number of phase-variable Type III R-M systems, which play a role in virulence. A growing number of these enzymes are being subjected to biochemical and genetic studies, which, when combined with ongoing structural analyses, promise to provide details for mechanisms of DNA recognition and catalysis