Latent-image formation in tabular AgBr grains: simulation studies

A simulation programme based on the nucleation-and-growth model of latent-image formation was used to study how trap depth and trap density at various tabular grain thicknesses affected quantum sensitivity and reciprocity failure. Using a 1.2x0.2 µm model ‘grain’, the unsensitized case was simulated with 0.05 eV traps located on both the face and the core of the grain, the latter to simulate the effect of twin planes on latent-image location. The trap densities were adjusted to achieve a higher internal speed than surface speed, as seen experimentally with the emulsion used to validate the simulation. To simulate the effects of chemical sensitization, these parameters were held fixed while edge traps of depths 0.2–0.6 eV were added at various trap densities for grain thicknesses of 50, 100 and 200 nm. All but the lowest trap densities at 0.2 eV changed the situation to complete or almost complete edge domination for latent-image location. Maximum efficiencies for latent-image formation were six to eight absorbed photons/grain for a 0.01 s exposure, although the trap density had to be decreased as the trap depth increased to achieve these maximum values. A decrease in efficiency with decreasing thickness as well as with decreasing diameter was seen for the lower trap depth values. These grain diameter and thickness effects disappeared for simulations using a 10^–6 s exposure, indicating that the decreasing efficiency at 0.01 s was due to differences in the onset of low-irradiance reciprocity failure. Reciprocity failure was simulated for chosen trap depth/density combinations. These data were compared with experimental reciprocity failure data to help validate the model. Reasonable agreement was obtained for trap depths in the range of those deduced from the experimental phase of the project. However, uncertainties regarding other parameters that affect the position of the reciprocity failure curve with respect to exposure time must be reduced before this agreement can be considered a validation of the model (Refer to PDF file for exact formulas)

Pathological mutations in PNKP trigger defects in DNA single-strand break repair but not DNA double-strand break repair

Hereditary mutations in polynucleotide kinase-phosphatase (PNKP) result in a spectrum of neurological pathologies ranging from neurodevelopmental dysfunction in microcephaly with early onset seizures (MCSZ) to neurodegeneration in ataxia oculomotor apraxia-4 (AOA4) and Charcot-Marie-Tooth disease (CMT2B2). Consistent with this, PNKP is implicated in the repair of both DNA single-strand breaks (SSBs) and DNA double-strand breaks (DSBs); lesions that can trigger neurodegeneration and neurodevelopmental dysfunction, respectively. Surprisingly, however, we did not detect a significant defect in DSB repair (DSBR) in primary fibroblasts from PNKP patients spanning the spectrum of PNKP-mutated pathologies. In contrast, the rate of SSB repair (SSBR) is markedly reduced. Moreover, we show that the restoration of SSBR in patient fibroblasts collectively requires both the DNA kinase and DNA phosphatase activities of PNKP, and the fork-head associated (FHA) domain that interacts with the SSBR protein, XRCC1. Notably, however, the two enzymatic activities of PNKP appear to affect different aspects of disease pathology, with reduced DNA phosphatase activity correlating with neurodevelopmental dysfunction and reduced DNA kinase activity correlating with neurodegeneration. In summary, these data implicate reduced rates of SSBR, not DSBR, as the source of both neurodevelopmental and neurodegenerative pathology in PNKP-mutated disease, and the extent and nature of this reduction as the primary determinant of disease severity

Materials Sciences and Applications

Precursor (Metal-organic decomposition (MOD)) inks are used to fabricate 2D and 3D printed conductive structures directly onto a substrate. By formulating a nanoalloy structure containing multiple metals, the opportunity to modify chemical and physical properties exists. In this paper, a copper-nickel bimetallic nanoalloy film was fabricated by mixing copper and nickel precursor inks and sintering them in vacuum. The individual elemental inks were formulated and characterized using SEM, EDS, and XRD. During thermal processing, elemental copper forms first and is followed by the formation of bimetallic copper-nickel alloy. The encapsulation of the underlying copper by the nickel-rich alloy provides excellent oxidation resistance. No change in film resistance was observed after the film was exposed to an oxygen plasma. Nanoalloy films printed using reactive metallic inks have a variety of important applications involving local control of alloy composition. Examples include facile formation of layered nanostructures, and electrical conductivity with oxidative stability

CytoCensus, mapping cell identity and division in tissues and organs using machine learning.

A major challenge in cell and developmental biology is the automated identification and quantitation of cells in complex multilayered tissues. We developed CytoCensus: an easily deployed implementation of supervised machine learning that extends convenient 2D 'point-and-click' user training to 3D detection of cells in challenging datasets with ill-defined cell boundaries. In tests on such datasets, CytoCensus outperforms other freely available image analysis software in accuracy and speed of cell detection. We used CytoCensus to count stem cells and their progeny, and to quantify individual cell divisions from time-lapse movies of explanted Drosophila larval brains, comparing wild-type and mutant phenotypes. We further illustrate the general utility and future potential of CytoCensus by analysing the 3D organisation of multiple cell classes in Zebrafish retinal organoids and cell distributions in mouse embryos. CytoCensus opens the possibility of straightforward and robust automated analysis of developmental phenotypes in complex tissues

Formation of Copper Nickel Bimetallic Nanoalloy Film Using Precursor Inks

Precursor (Metal-organic decomposition (MOD)) inks are used to fabricate 2D and 3D printed conductive structures directly onto a substrate. By formulating a nanoalloy structure containing multiple metals, the opportunity to modify chemical and physical properties exists. In this paper, a copper-nickel bimetallic nanoalloy film was fabricated by mixing copper and nickel precursor inks and sintering them in vacuum. The individual elemental inks were formulated and characterized using SEM, EDS, and XRD. During thermal processing, elemental copper forms first and is followed by the formation of bimetallic copper-nickel alloy. The encapsulation of the underlying copper by the nickel-rich alloy provides excellent oxidation resistance. No change in film resistance was observed after the film was exposed to an oxygen plasma. Nanoalloy films printed using reactive metallic inks have a variety of important applications involving local control of alloy composition. Examples include facile formation of layered nanostructures, and electrical conductivity with oxidative stability

Efficient single-strand break repair requires binding to both poly(ADP-ribose) and DNA by the central BRCT domain of XRCC1

XRCC1 accelerates repair of DNA single-strand breaks by acting as a scaffold protein for the recruitment of Pol-beta, LigIII-alpha and end-processing factors such as PNKP and APTX. XRCC1 itself is recruited to DNA damage through interaction of its central BRCT domain with poly-(ADP-ribose) chains generated by PARP1 or PARP2. XRCC1 is believed to interact directly with DNA at sites of damage, but the molecular basis for this interaction within XRCC1 remains unclear. We now show that the central BRCT domain simultaneously mediates interaction of XRCC1 with poly-(ADP-ribose) and DNA, through separate and non-overlapping binding sites on opposite faces of the domain. Mutation of residues within the DNA binding site, which includes the site of a common disease-associated human polymorphism, affects DNA binding of this XRCC1 domain in vitro, and impairs XRCC1 recruitment and retention at DNA damage and repair of single-strand breaks in vivo

Pathogenic ARH3 mutations result in ADP-ribose chromatin scars during DNA strand break repair

Neurodegeneration is a common hallmark of individuals with hereditary defects in DNA single-strand break repair; a process regulated by poly(ADP-ribose) metabolism. Recently, mutations in the ARH3 (ADPRHL2) hydrolase that removes ADP-ribose from proteins have been associated with neurodegenerative disease. Here, we show that ARH3-mutated patient cells accumulate mono(ADP-ribose) scars on core histones that are a molecular memory of recently repaired DNA single-strand breaks. We demonstrate that the ADP-ribose chromatin scars result in reduced endogenous levels of important chromatin modifications such as H3K9 acetylation, and that ARH3 patient cells exhibit measurable levels of deregulated transcription. Moreover, we show that the mono(ADP-ribose) scars are lost from the chromatin of ARH3-defective cells in the prolonged presence of PARP inhibition, and concomitantly that chromatin acetylation is restored to normal. Collectively, these data indicate that ARH3 can act as an eraser of ADP-ribose chromatin scars at sites of PARP activity during DNA single-strand break repair