Calcite surface structure and reactivity: molecular dynamics simulations and macroscopic surface modelling of the calcite-water interface.

Calcite-water interactions are important not only in carbon sequestration and the global carbon cycle, but also in contaminant behaviour in calcite-bearing host rock and in many industrial applications. Here we quantify the effect of variations in surface structure on calcite surface reactivity. Firstly, we employ classical Molecular Dynamics simulations of calcite surfaces containing an etch pit and a growth terrace, to show that the local environment in water around structurally different surface sites is distinct.

Monosomy 9pter and trisomy 9q34.11qter in two sisters due to a maternal pericentric inversion.

Pericentric inversions of chromosome 9 leading to unbalanced live-born offspring are relatively rare and so far only four cases have been reported. Here we present two sisters with an unbalanced recombinant chromosome 9 which resulted from a large maternal pericentric inversion inv(9)(p24.3q34.

Copy number variants in a sample of patients with psychotic disorders: is standard screening relevant for actual clinical practice?

With the introduction of new genetic techniques such as genome-wide array comparative genomic hybridization, studies on the putative genetic etiology of schizophrenia have focused on the detection of copy number variants (CNVs), ie, microdeletions and/or microduplications, that are estimated to be present in up to 3% of patients with schizophrenia. In this study, out of a sample of 100 patients with psychotic disorders, 80 were investigated by array for the presence of CNVs. The assessment of the severity of psychiatric symptoms was performed using standardized instruments and ICD-10 was applied for diagnostic classification.

A 380-kb Duplication in 7p22.3 Encompassing the LFNG Gene in a Boy with Asperger Syndrome.

De novo genomic aberrations are considered an important cause of autism spectrum disorders. We describe a de novo 380-kb gain in band p22.3 of chromosome 7 in a patient with Asperger syndrome.

Interpretation of clinical relevance of X-chromosome copy number variations identified in a large cohort of individuals with cognitive disorders and/or congenital anomalies.

Genome-wide array studies are now routinely being used in the evaluation of patients with cognitive disorders (CD) and/or congenital anomalies (CA). Therefore, inevitably each clinician is confronted with the challenging task of the interpretation of copy number variations detected by genome-wide array platforms in a diagnostic setting. Clinical interpretation of autosomal copy number variations is already challenging, but assessment of the clinical relevance of copy number variations of the X-chromosome is even more complex.

Mg/Ca partitioning between aqueous solution and aragonite mineral: a molecular dynamics study.

We have calculated the concentrations of Mg in the bulk and surfaces of aragonite CaCO(3) in equilibrium with aqueous solution, based on molecular dynamics simulations and grand-canonical statistical mechanics. Mg is incorporated in the surfaces, in particular in the (001) terraces, rather than in the bulk of aragonite particles. However, the total Mg content in the bulk and surface of aragonite particles was found to be too small to account for the measured Mg/Ca ratios in corals.

Diagnostic interpretation of array data using public databases and internet sources.

The range of commercially available array platforms and analysis software packages is expanding and their utility is improving, making reliable detection of copy-number variants (CNVs) relatively straightforward. Reliable interpretation of CNV data, however, is often difficult and requires expertise. With our knowledge of the human genome growing rapidly, applications for array testing continuously broadening, and the resolution of CNV detection increasing, this leads to great complexity in interpreting what can be daunting data.

Meiotic errors followed by two parallel postzygotic trisomy rescue events are a frequent cause of constitutional segmental mosaicism.

Structural copy number variation (CNV) is a frequent cause of human variation and disease. Evidence is mounting that somatic acquired CNVs are prevalent, with mosaicisms of large segmental CNVs in blood found in up to one percent of both the healthy and patient populations. It is generally accepted that such constitutional mosaicisms are derived from postzygotic somatic mutations.

Genome-wide arrays in routine diagnostics of hematological malignancies.

Over the last three decades, cytogenetic analysis of malignancies has become an integral part of disease evaluation and prediction of prognosis or responsiveness to therapy. In most diagnostic laboratories, conventional karyotyping, in conjunction with targeted fluorescence in situ hybridization analysis, is routinely performed to detect recurrent aberrations with prognostic implications. However, the genetic complexity of cancer cells requires a sensitive genome-wide analysis, enabling the detection of small genomic changes in a mixed cell population, as well as of regions of homozygosity.

Non-targeted whole genome 250K SNP array analysis as replacement for karyotyping in fetuses with structural ultrasound anomalies: evaluation of a one-year experience.

Objective: We evaluated both clinical and laboratory aspects of our new strategy offering quantitative fluorescence (QF)-PCR followed by non-targeted whole genome 250K single-nucleotide polymorphism array analysis instead of routine karyotyping for prenatal diagnosis of fetuses with structural anomalies.

Methods: Upon the detection of structural fetal anomalies, parents were offered a choice between QF-PCR and 250K single-nucleotide polymorphism array analysis (QF/array) or QF-PCR and routine karyotyping (QF/karyo).

Results: Two hundred twenty fetal samples were included.

Two families with sibling recurrence of the 17q21.31 microdeletion syndrome due to low-grade mosaicism.

The 17q21.31 microdeletion syndrome is characterised by intellectual disability, epilepsy, distinctive facial dysmorphism, and congenital anomalies. To date, all individuals reported with this syndrome have been simplex patients, resulting from de novo deletions.

A density functional theory study of structural, mechanical and electronic properties of crystalline phosphorus pentoxide.

Quantum mechanical calculations of single crystal phosphorus pentoxide (P(2)O(5)) have been conducted using the plane-wave ultrasoft pseudopotential technique based on the density functional theory (DFT), in the generalized gradient approximation, with dispersive correction (DFT-D). The implementation of the dispersive correction is shown to improve significantly the structural agreement with experiment, compared to standard plane-wave DFT. The second order elastic constants for the o'(P(2)O(5))(∞) and o(P(2)O(5)) orthorhombic phases were obtained from a polynomial fit to the calculated energy-strain relation.

A novel microdeletion syndrome at 3q13.31 characterised by developmental delay, postnatal overgrowth, hypoplastic male genitals, and characteristic facial features.

Background: Congenital deletions affecting 3q11q23 have rarely been reported and only five cases have been molecularly characterised. Genotype-phenotype correlation has been hampered by the variable sizes and breakpoints of the deletions. In this study, 14 novel patients with deletions in 3q11q23 were investigated and compared with 13 previously reported patients.

A de novo 3.57 Mb microdeletion in 8q12.3q13.2 in a patient with mild intellectual disability and epilepsy.

A female patient, nine years of age, is reported with a history characterized by delay of psychomotor and speech development, mild to moderate intellectual disability and persistent sleep disturbances since the age of two. The patient showed facial dysmorphisms, a pectus excavatum and a sandal gap. Apart from lowered intelligence, neuropsychological functioning disclosed impaired attentional capacities and executive control as well as weak motor skills.

Mixing thermodynamics of the calcite-structured (Mn,Ca)CO3 solid solution: a computer simulation study.

We have employed atomistic simulation techniques to investigate the thermodynamics of mixing in the solid solutions of calcite (CaCO(3)) and rhodochrosite (MnCO(3)). Our calculations show that the fully disordered solid solution has positive enthalpies of mixing for the entire range of compositions, which confirm recent experiments. The consideration of a small degree of ordering in the simulations leads to mixing enthalpies in quantitative agreement with experimental measurements.

De novo copy number variants associated with intellectual disability have a paternal origin and age bias.

Background: De novo mutations and structural rearrangements are a common cause of intellectual disability (ID) and other disorders with reduced or null reproductive fitness. Insight into the genomic and environmental factors predisposing to the generation of these de novo events is therefore of significant clinical importance.

Methods: This study used information from single nucleotide polymorphism microarrays to determine the parent-of-origin of 118 rare de novo copy number variations (CNVs) detected in a cohort of 3443 patients with ID.

SNP array analysis in constitutional and cancer genome diagnostics--copy number variants, genotyping and quality control.

Array-based comparative genomic hybridization analysis of genomic DNA was first applied in postnatal diagnosis for patients with intellectual disability (ID) and/or congenital anomalies (CA). Genome-wide single-nucleotide polymorphism (SNP) array analysis was subsequently implemented as the first line diagnostic test for ID/CA patients in our laboratory in 2009, because its diagnostic yield is significantly higher than that of routine cytogenetic analysis. In addition to the detection of copy number variations, the genotype information obtained with SNP array analysis enables the detection of stretches of homozygosity and thereby the possible identification of recessive disease genes, mosaic aneuploidy, or uniparental disomy.

Parental insertional balanced translocations are an important cause of apparently de novo CNVs in patients with developmental anomalies.

In several laboratories, genome-wide array analysis has been implemented as the first tier diagnostic test for the identification of copy number changes in patients with mental retardation and/or congenital anomalies. The identification of a pathogenic copy number variant (CNV) is not only important to make a proper diagnosis but also to enable the accurate estimation of the recurrence risk to family members. Upon the identification of a de novo interstitial loss or gain, the risk recurrence is considered very low.

Pierpont syndrome: a collaborative study.

Pierpont syndrome is a multiple congenital anomaly syndrome with learning disability first described in 1998. There are only three patients with Pierpont syndrome who have previously been published in the literature. Details of a series of patients with features of this condition were therefore obtained retrospectively to better characterize its key features.

Binding of glycosaminoglycan saccharides to hydroxyapatite surfaces: A density functional theory study.

Density functional theory calculations implemented by the SIESTA code are used to study the interactions of the saccharides -acetylgalactosamine (GalNAc) and glucuronic acid (GlcA) with the (0001) and [Formula: see text] surfaces of the mineral hydroxyapatite (HAP). GalNAc and GlcA are the constituent monosaccharides of chondroitin, which is a glycosaminoglycan found in bone and cartilage, and whose interactions with HAP have been implicated as a controlling factor in the process of biomineralisation. Geometry optimisation calculations are used to identify low energy adsorption structures of the monosaccharides on the HAP surfaces, and to calculate the corresponding adsorption energies.

Balanced into array: genome-wide array analysis in 54 patients with an apparently balanced de novo chromosome rearrangement and a meta-analysis.

High-resolution genome-wide array analysis enables detailed screening for cryptic and submicroscopic imbalances of microscopically balanced de novo rearrangements in patients with developmental delay and/or congenital abnormalities. In this report, we added the results of genome-wide array analysis in 54 patients to data on 117 patients from seven other studies. A chromosome imbalance was detected in 37% of all patients with two-breakpoint rearrangements.

A molecular dynamics study of the interprotein interactions in collagen fibrils.

Molecular dynamics simulations of collagen are used to investigate at the atomistic level the nature of the interprotein interactions that are present within a collagen fibril, and which are responsible for the fibril's thermodynamic stability. Simulations both of a collagen fibril and of a fully solvated tropcollagen are compared in order to study the interactions that arise between the proteins upon the process of fibrillogenesis. The interactions studied include direct interprotein hydrogen bonds, water-mediated interprotein hydrogen bonds, and hydrophobic interactions.

Vacancy ordering and electronic structure of γ-Fe₂O₃ (maghemite): a theoretical investigation.

The crystal structure of the iron oxide γ-Fe₂O₃ is usually reported in either the cubic system (space group P4(3)32) with partial Fe vacancy disorder or in the tetragonal system (space group P4(1)2(1)2) with full site ordering and c/a≈3. Using a supercell of the cubic structure, we obtain the spectrum of energies of all the ordered configurations which contribute to the partially disordered P4(3)32 cubic structure. Our results show that the configuration with space group P4(1)2(1)2 is indeed much more stable than the others, and that this stability arises from a favourable electrostatic contribution, as this configuration exhibits the maximum possible homogeneity in the distribution of iron cations and vacancies.