A scanning tunnelling microscopy study of C and N adsorption phases on the vicinal Ni(100) surfaces Ni(810) and Ni(911)

The influence of N and C chemisorption on the morphology and local structure of nominal Ni(810) and Ni(911) surfaces, both vicinal to (100) but with [001] and 011¯ step directions, respectively, has been investigated using scanning tunnelling microscopy (STM) and low energy electron diffraction. Ni(911) undergoes substantial step bunching in the presence of both adsorbates, with the (911)/N surface showing (411) facets, whereas for Ni(810), multiple steps 2–4 layers high are more typical. STM atomic-scale images show the (2×2)pg ‘clock’ reconstruction on the (100) terraces of the (810) surfaces with both C and N, although a second c(2×2) structure, most readily reconciled with a ‘rumpling’ reconstruction, is also seen on Ni(810)/N. On Ni(911), the clock reconstruction is not seen on the (100) terraces with either adsorbate, and these images are typified by protrusions on a (1×1) mesh. This absence of clock reconstruction is attributed to the different constraints imposed on the lateral movements of the surface Ni atoms adjacent to the up-step edge of the terraces with a [011] step direction

The local adsorption structure of benzene on Si(001)-(2 × 1): a photoelectron diffraction investigation

Scanned-energy mode C 1s photoelectron diffraction has been used to investigate the local adsorption geometry of benzene on Si(001) at saturation coverage and room temperature. The results show that two different local bonding geometries coexist, namely the 'standard butterfly' (SB) and 'tilted bridge' (TB) forms, with a composition of 58 ± 29% of the SB species. Detailed structural parameter values are presented for both species including Si–C bond lengths. On the basis of published measurements of the rate of conversion of the SB to the TB form on this surface, we estimate that the timescale of our experiment is sufficient for achieving equilibrium, and in this case our results indicate that the difference in the Gibbs free energy of adsorption, ΔG(TB)−ΔG(SB), is in the range −0.023 to +0.049 eV. We suggest, however, that the relative concentration of the two species may also be influenced by a combination of steric effects influencing the kinetics, and a sensitivity of the adsorption energies of the adsorbed SB and TB forms to the nature of the surrounding benzene molecules

Structural precursor to adsorbate-induced reconstruction: C on Ni(100)

The local structure around adsorbed carbon atoms on Ni(100) has been determined at low coverage as well as in the 0.5 monolayer (2×2)p4g “clock” reconstruction by scanned energy mode photoelectron diffraction. At low coverage, there is no radial strain of the Ni atoms surrounding the adsorbed carbon, contrary to previous suggestions. None of the C-Ni near-neighbor distances are changed by reconstruction, but the Ni-Ni nearest-neighbor distance in the top layer increases significantly, showing that the adsorbate-induced compressive stress is associated with Ni-Ni, rather than Ni-C, repulsion

Local adsorption geometry of acetylene on Si(100)(2×1)

Using C 1s scanned-energy-mode photoelectron diffraction the local adsorption geometry of acetylene on the Si(100)(2x1) surface has been determined and the results are compared with those of a similar study of ethylene adsorption on this surface. Both molecules bond to the surface along the Si-Si dimers with the C-C bonds parallel to the surface such that the C atoms are in off-atop sites relative to the Si dimer atoms. In both cases the Si-Si bond length (2.36±0.21 Å for ethylene and 2.44±0.58 Å for acetylene) is compatible only with the dimer remaining intact after adsorption and not with the Si-Si distance of an ideally terminated undimerized Si(100) surface (3.84 Å)

Structural analysis of Pt(1 1 1)c(√3 × 5)rect.–CO using photoelectron diffraction

Core level shift scanned-energy mode photoelectron diffraction using the two distinct components of the C 1s emission has been used to determine the structure of the Pt(1 1 1)c(√3 × 5)rect.–CO phase formed by 0.6 ML of adsorbed CO. The results confirm earlier assignments of these components to CO in atop and bridging sites, further confirm that the best structural model involves a 2:1 occupation ratio of these two sites, and provides quantitative structural parameter values. In particular the Pt–C chemisorption bondlengths for the atop and bridging sites are, respectively, 1.86 ± 0.02 Å and 2.02 ± 0.04 Å. These values are closely similar to those found in the 0.5 ML coverage c(4 × 2) phase, involving an atop:bridge occupation ratio of 1:1, obtained in earlier quantitative low energy electron diffraction studies. The results also indicate a clear tilt of the molecular axis of atop CO species in this compression phase, consistent with the finding of an earlier electron-stimulated desorption ion angular distribution investigatio

Complete Experimental Structure Determination of the p(3x2)pg Phase of Glycine on Cu{110}

We present a quantitative low energy electron diffraction (LEED) surface-crystallograpic study of the complete adsorption geometry of glycine adsorbed on Cu{110} in the ordered p(3×2) phase. The glycine molecules form bonds to the surface through the N atoms of the amino group and the two O atoms of the de-protonated carboxylate group, each with separate Cu atoms such that every Cu atom in the first layer is involved in a bond. Laterally, N atoms are nearest to the atop site (displacement 0.41 Å). The O atoms are asymmetrically displaced from the atop site by 0.54 Å and 1.18 Å with two very different O-Cu bond lengths of 1.93 Å and 2.18 Å. The atom positions of the upper-most Cu layers show small relaxations within 0.07 Å of the bulk-truncated surface geometry. The unit cell of the adsorbate layer consists of two glycine molecules, which are related by a glide-line symmetry operation. This study clearly shows that a significant coverage of adsorbate structures without this glide-line symmetry must be rejected, both on the grounds of the energy dependence of the spot intensities (LEED-IV curves) and of systematic absences in the LEED pattern

Pediatric cataract, myopic astigmatism, familial exudative vitreoretinopathy and primary open-angle glaucoma co-segregating in a family

Purpose: To describe an Australian pedigree of European descent with a variable autosomal dominant phenotype of: pediatric cortical cataract (CC), asymmetric myopia with astigmatism, familial exudative vitreoretinopathy (FEVR), and primary open-angle glaucoma (POAG). Methods: Probands with CC, FEVR, and POAG were enrolled in three independent genetic eye studies in Tasmania. Genealogy confirmed these individuals were closely related and subsequent examination revealed 11 other family members with some or all of the associated disorders. Results: Twelve individuals had CC thought to be of childhood onset, with one child demonstrating progressive lenticular opacification. One individual had severe retinal detachment while five others had dragged retinal vessels. Seven individuals had POAG. Seven individuals had myopia in at least one eye ≤-3 Diopters. DNA testing excluded mutations in myocilin, trabecular meshwork inducible glucocorticoid response (MYOC) and tetraspanin 12 (TSPAN12). Haplotype analysis excluded frizzled family receptor 4 (FZD4) and low density lipoprotein receptor-related protein 5 (LRP5), but only partly excluded EVR3. Multipoint linkage analysis revealed multiple chromosomal single-nucleotide polymorphisms (SNPs) of interest, but no statistically significant focal localization. Conclusions: This unusual clustering of ophthalmic diseases suggests a possible single genetic cause for an apparently new cataract syndrome. This family’s clinical ocular features may reflect the interplay between retinal disease with lenticular changes and axial length in the development of myopia and glaucoma

Am J Hum Genet

Fuhrmann syndrome and the Al-Awadi/Raas-Rothschild/Schinzel phocomelia syndrome are considered to be distinct limb-malformation disorders characterized by various degrees of limb aplasia/hypoplasia and joint dysplasia in humans. In families with these syndromes, we found homozygous missense mutations in the dorsoventral-patterning gene WNT7A and confirmed their functional significance in retroviral-mediated transfection of chicken mesenchyme cell cultures and developing limbs. The results suggest that a partial loss of WNT7A function causes Fuhrmann syndrome (and a phenotype similar to mouse Wnt7a knockout), whereas the more-severe limb truncation phenotypes observed in Al-Awadi/Raas-Rothschild/Schinzel phocomelia syndrome result from null mutations (and cause a phenotype similar to mouse Shh knockout). These findings illustrate the specific and conserved importance of WNT7A in multiple aspects of vertebrate limb development

Targeted nanopore sequencing enables complete characterisation of structural deletions initially identified using exon-based short-read sequencing strategies

Background The widespread adoption of exome sequencing has greatly increased the rate of genetic diagnosis for inherited conditions. However, the detection and validation of large deletions remains challenging. While numerous bioinformatics approaches have been developed to detect deletions from whole - exome sequencing and targeted panels, further work is typically required to define the physical breakpoints or integration sites. Accurate characterisation requires either expensive follow - up whole - genome sequencing or the time - consuming, laborious process of PCR walking, both of which are challenging when dealing with the repeat sequences which frequently intersect deletion breakpoints. The aim of this study was to develop a cost-effective, long-range sequencing method to characterise deletions. Methods Genomic DNA was amplified with primers spanning the deletion using long-range PCR and the products purified. Sequencing was performed on MinION flongle flowcells. The resulting fast5 files were basecalled using Guppy, trimmed using Porechop and aligned using Minimap2. Filtering was performed using NanoFilt. Nanopore sequencing results were verified by Sanger sequencing. Results Four cases with deletions detected following comparative read-depth analysis of targeted short-read sequencing were analysed. Nanopore sequencing defined breakpoints at the molecular level in all cases including homozygous breakpoints in EYS, CNGA1 and CNGB1 and a heterozygous deletion in PRPF31. All breakpoints were verified by Sanger sequencing. Conclusions In this study, a quick, accurate and cost - effective method is described to characterise deletions identified from exome, and similar data, using nanopore sequencing

The dimers stay intact: a quantitative photoelectron study of the adsorption system Si{100} (2x1)-C2H4

Using the technique of photoelectron diffraction in the scanned energy mode we show that the Si dimer separation on the Si{100} surface following the adsorption of ethene (ethylene) is 2.36(±0.21) A. This value is only very slightly larger than on the clean surface and shows that the dimer remains intact, thus providing a clear quantitative experimental resolution of a long controversy in the literature. The C-C and C-Si separations are 1.62±0.08 A and 1.90±0.01 A, respectively, the former indicating a bond order of less than one