Molecular characterization and cancer risk associated with BRCA1 and BRCA2 splice site variants identified in multiple-case breast cancer families

Genetic screening of women from multiple-case breast cancer families and other research-based endeavors have identified an extensive collection of germline variations of BRCA1 and BRCA2 that can be classified as deleterious and have clinical relevance. For some variants, such as those in the conserved intronic splice site regions which are highly likely to alter splicing, it is not possible to classify them based on the identified DNA sequence variation alone. We studied 11 multiple-case breast cancer families carrying seven distinct splice site region genetic alterations in BRCA1 or BRCA2 (BRCA1, c.IVS6-2delA, c.IVS9-2A>C, c.IVS4-1G>T, c.IVS20+1G>A and BRCA2, c.IVS17-1G>C, c.IVS20+1G>A, c.IVS7-1G>A) and applied SpliceSiteFinder to predict possible changes in efficiency of splice donor and acceptor sites, characterized the transcripts, and estimated the average age-specific cumulative risk (penetrance) using a modified segregation analysis. SpliceSiteFinder predicted and we identified transcipts that illustrated that all variants caused exon skipping, and all but two led to frameshifts. The risks of breast cancer to age 70 yrs, averaged over all variants, over BRCA1 variants alone, and over BRCA2 variants alone, were 73% (95% confidence interval 47-93), 64% (95%CI 28-96) and 79% (95%CI 48-98) respectively (all P

Characterization of heparin-binding site of tissue transglutaminase:its importance in cell surface targeting, matrix deposition, and cell signaling

Tissue transglutaminase (TG2) is a multifunctional Ca2+ activated protein crosslinking enzyme secreted into the extracellular matrix (ECM), where it is involved in wound healing and scarring, tissue fibrosis, celiac disease and metastatic cancer. Extracellular TG2 can also facilitate cell adhesion important in wound healing through a non-transamidating mechanism via its association with fibronectin (FN), heparan sulphates (HS) and integrins. Regulating the mechanism how TG2 is translocated into the ECM therefore provides a strategy for modulating these physiological and pathological functions of the enzyme. Here, through molecular modelling and mutagenesis we have identified the HS binding site of TG2 202KFLKNAGRDCSRRSSPVYVGR222. We demonstrate the requirement of this binding site for translocation of TG2 into the ECM through a mechanism involving cell surface shedding of HS. By synthesizing a peptide NPKFLKNAGRDCSRRSS corresponding to the HS binding site within TG2, we also demonstrate how this mimicking peptide can in isolation compensate the RGD-induced loss of cell adhesion on FN via binding to syndecan-4, leading to activation of PKCa, pFAK-397 and ERK1/2 and the subsequent formation of focal adhesions and actin cytoskeleton organization. A novel regulatory mechanism for TG2 translocation into the extracellular compartment that depends upon TG2 conformation and the binding of HS is proposed.

Characterization of medieval glass artefacts from Miranduolo site, Chiusdino, Italy

This archaeovitreological study deals with artefacts of Miranduolo site, Tuscany region (Italy), dated 1250-1350 AD. The Miranduolo site is a medieval hill-village dated from 7th to 14th century. The information obtained reveal that Miranduolo was under control of noble families, which displayed the social, economic and political power. It is marked by controlling the farmers and metal workers on the site, as well as having control over agricultural surpluses. No in situ glass workshop has been recovered, implying that the glass artefacts were imported. One aim of this work is application of SEM-EDS to visualize textural characteristics and thickness of the pristine glass and corrosion layers. Preliminary qualification and semi-quantification of major and minor chemical elements will provide the data on the glass group present and fluxes employed. The data obtained will be integrated with the one obtained by more sensitive techniques such as PIXE/PIGE and LA-ICP-MS. Twenty cross-sections of transparent glasses (colorless, azure, and different hues of yellow and) have been analyzed by VP-SEM. All the analyzed glasses display a homogenous matrix. Only four samples (MD 24, MD 139, MD 143, MD 259) show corrosion layers of various thickness with 2.25μm, 136-500 μm, 26.8 μm and 17.01 μm. EDS linescan analyses indicate strong depletion in the corrosion layers of Na and K, while Ca depletes to a minor extent. In general, both glass composition and the burial conditions were favorable for preservation. Samples can be classified as mainly plant ash Na-Ca-Si glasses made with both unpurified and purified Levantine ash. Only sample MD 243 is made from Barilla plant ash. Sample MD 139 cannot be classified into main compositional groups as K2O is 1.33 wt% and MgO 5.92 wt%. In 8 samples MnO content is lower than 0.8 wt%, meaning that in these samples MnO is naturally present. In other 12 samples, MnO above 0.8 wt% indicates deliberate addition as a decolorant agent to intentionally obtain different hues or the amount added was not successful in making the glass transparent. The results considering fluxes are compatible with archaeovitreological study from contemporary primary glass workshops in Tuscany. For determining the provenance of silica sources, further analysis with more sensitive techniques has to be carried out; Resumo: Este estudo “arqueovitreologia” lida com artefatos do local Miranduolo, região da Toscana (Itália), datados de 1250-1350 AD. O sitio de Miranduolo é uma colina vila medieval datada do séc.VII ao séc.XIV. As informações obtidas revelam que Miranduolo estava sob o controle de famílias nobres, que exibiu o poder social, económico e político. É marcado por controlar os agricultores e trabalhadores do metal no sitio, bem como ter controlo sobre os excedentes agrícolas. Não há na oficina de vidro in situ foi recuperado, o que implica que os artefactos de vidro foram importados. Um dos objetivos deste trabalho é a aplicação de SEM-EDS para visualizar características de textura e espessura das camadas de corrosão do vidro também como da áreas originais. qualificação preliminar e semi-quantificação de maiores e menores elementos químicos irá fornecer os dados sobre o grupo presente vidro e fluxos empregado. Os dados obtidos são integrados com os dados obtidos por meio de técnicas mais sensíveis, como PIXE / PIGE e LA-ICP-MS. Vinte secções transversais de vidros transparentes (incolor, azul celeste, e diferentes tons de amarelo) foram analisados por VP-SEM. Todos os vidros analisados exibir uma matriz homogénea. Apenas quatro amostras (MD 24, MD 139, MD 143, MD 259) mostram camadas de corrosão de várias espessuras com 2.25μm, 136-500μm, 26,8μm e 17,01μm. Análises Linescan EDS indicam forte esgotamento nas camadas de corrosão de Na e K, enquanto Ca esgota, em menor grau. Em geral, tanto a composição de vidro e as condições de depósito foram favoráveis para a preservação. As amostras podem ser classificados como vidros principalmente Na-Ca-Si feitas com cinzas de plantas do tipo levantino, não purificada e purificada. Apenas a amostra MD 243 é feita a partir de cinzas vegetais tipo “Barilla”. A amostra MD 139 não pode ser classificada em grupos principais de composição porque K2O é 1,33% em peso e MgO 5,92% em peso. Em 8 amostras, o teor de MnO é menor do que 0,8% em peso, o que significa que nestas amostras MnO está naturalmente presente. Em outras 12 amostras, MnO acima de 0,8% em peso indica adição intencional como um agente de colorante para obter intencionalmente diferentes matizes ou o valor acrescentado não foi bem sucedido em fazer o vidro transparente. Os resultados, considerando os fluxos são compatíveis com o estudo “arqueovitreologico” com as principais oficinas de vidro contemporâneos na Toscana. Para determinar a origem das fontes de sílica, uma análise mais aprofundada com técnicas mais sensíveis tem de ser levada a cabo.

Development of descriptor tools for the characterization of Australian sugar mill evaporator scale

Cleaning of sugar mill evaporators is an expensive exercise. Identifying the scale components assists in determining which chemical cleaning agents would result in effective evaporator cleaning. The current methods (based on x-ray diffraction techniques, ion exchange/high performance liquid chromatography and thermogravimetry/differential thermal analysis) used for scale characterisation are difficult, time consuming and expensive, and cannot be performed in a conventional analytical laboratory or by mill staff. The present study has examined the use of simple descriptor tests for the characterisation of Australian sugar mill evaporator scales. Scale samples were obtained from seven Australian sugar mill evaporators by mechanical means. The appearance, texture and colour of the scale were noted before the samples were characterised using x-ray fluorescence and x-ray powder diffraction to determine the compounds present. A number of commercial analytical test kits were used to determine the phosphate and calcium contents of scale samples. Dissolution experiments were carried out on the scale samples with selected cleaning agents to provide relevant information about the effect the cleaning agents have on different evaporator scales. Results have shown that by simply identifying the colour and the appearance of the scale, the elemental composition and knowing from which effect the scale originates, a prediction of the scale composition can be made. These descriptors and dissolution experiments on scale samples can be used to provide factory staff with an on-site rapid process to predict the most effective chemicals for chemical cleaning of the evaporators.

Characterization of particle number concentrations and PM2.5 in a school : influence of outdoor air pollution on indoor air

Background, Aim and Scope The impact of air pollution on school children’s health is currently one of the key foci of international and national agencies. Of particular concern are ultrafine particles which are emitted in large quantities, contain large concentrations of toxins and are deposited deeply in the respiratory tract. Materials and methods In this study, an intensive sampling campaign of indoor and outdoor airborne particulate matter was carried out in a primary school in February 2006 to investigate indoor and outdoor particle number (PN) and mass concentrations (PM2.5), and particle size distribution, and to evaluate the influence of outdoor air pollution on the indoor air. Results For outdoor PN and PM2.5, early morning and late afternoon peaks were observed on weekdays, which are consistent with traffic rush hours, indicating the predominant effect of vehicular emissions. However, the temporal variations of outdoor PM2.5 and PN concentrations occasionally showed extremely high peaks, mainly due to human activities such as cigarette smoking and the operation of mower near the sampling site. The indoor PM2.5 level was mainly affected by the outdoor PM2.5 (r = 0.68, p<0.01), whereas the indoor PN concentration had some association with outdoor PN values (r = 0.66, p<0.01) even though the indoor PN concentration was occasionally influenced by indoor sources, such as cooking, cleaning and floor polishing activities. Correlation analysis indicated that the outdoor PM2.5 was inversely correlated with the indoor to outdoor PM2.5 ratio (I/O ratio) (r = -0.49, p<0.01), while the indoor PN had a weak correlation with the I/O ratio for PN (r = 0.34, p<0.01). Discussion and Conclusions The results showed that occupancy did not cause any major changes to the modal structure of particle number and size distribution, even though the I/O ratio was different for different size classes. The I/O curves had a maximum value for particles with diameters of 100 – 400 nm under both occupied and unoccupied scenarios, whereas no significant difference in I/O ratio for PM2.5 was observed between occupied and unoccupied conditions. Inspection of the size-resolved I/O ratios in the preschool centre and the classroom suggested that the I/O ratio in the preschool centre was the highest for accumulation mode particles at 600 nm after school hours, whereas the average I/O ratios of both nucleation mode and accumulation mode particles in the classroom were much lower than those of Aitken mode particles. Recommendations and Perspectives The findings obtained in this study are useful for epidemiological studies to estimate the total personal exposure of children, and to develop appropriate control strategies for minimizing the adverse health effects on school children.

Thin-film elemental analyses for precise characterization of minerals

The Analytical Electron Microscope (AEM), with which secondary X-ray emission from a thin (<150nm), electron-transparent material is measured, has rapidly become a versatile instrument for qualitative and quantitative elemental analyses of many materials, including minerals. With due regard for sources of error in experimental procedures, it is possible to obtain high spatial resolution (~20nm diameter) and precise elemental analyses (~3% to 5% relative) from many silicate minerals. In addition, by utilizing the orientational dependence of X-ray emission for certain multi-substituted crystal structures, site occupancies for individual elements within a unit cell can be determined though with lower spatial resolution. The relative ease with which many of these compositional data may be obtained depends in part on the nature of the sample, but, in general, is comparable to other solid state analytical techniques such as X-ray diffraction and electron microprobe analysis. However, the improvement in spatial resolution obtained with the AEM (up to two orders of magnitude in analysis diameter) significantly enhances interpretation of fine-grained assemblages in many terrestrial or extraterrestrial rocks.

Infrared and Raman spectroscopic characterization of the phosphate mineral leucophosphite - K(Fe3+)2(PO4)2(OH)·2(H2O)

The phosphate mineral leucophosphite K(Fe2)3þ(PO4)2(OH) · 2H2O has been characterized by SEM-EDS, Raman, and infrared spectro- scopic measurements. The mineral is predominantly a K and Fe phosphate with some minor substitution of Al in the Fe3þ site. Raman bands at 994 and 1058 cm-1 are assigned to the symmetric stretching modes of PO3- and HPO2- units. The Raman bands at 1104, 1135, and 1177 cm-1 are assigned to the PO3- and HPO2- antisymmetric stretching modes. Raman and infrared spectra in the 2600–3800 cm-1 region show a complex set of overlapping bands, which may be resolved into the component bands. The Raman bands observed at 3325, 3355, and 3456 cm-1 are attributed to water stretching vibrations, and in the infrared spectrum, bands at 3237, 3317, and 3453 cm-1 are assigned to water stretching bands.

Synthesis and spectroscopic characterization of copper zinc aluminum nanoferrite particles

Copper doped zinc aluminium ferrites are synthesized by the solid-state reaction route is cubic crystalline with unit cell parameter varying from 8.39 to 8.89 Å. TEM pictures clearly indicating that fundamental unit is composed of octahedral and tetrahedral blocks and joined strongly shown in (a). EPR spectra is compositional dependent at lower Al/Cu concentration EPR spectra is due to Fe3+ and at a higher content of Al/Cu the EPR spectra is due to Cu2+. Absence of EPR spectra at room temperature indicates that the sample is perfectly ferromagnetic. EPR results at low temperature indicate that the sample is paramagnetic, and that copper is placed in the tetragonal elongation (B) site with magnetically non-equivalent ions in the unit cell having strong exchange coupling between them. This is shown in (b). (a) TEM image of ferrite with x = 0.15. (b) EPR spectrum of ferrite with x = 0.75.

Raman and infrared spectroscopic characterization of the silicate mineral lamprophyllite

The mineral lamprophyllite is fundamentally a silicate based upon tetrahedral siloxane units with extensive substitution in the formula. Lamprophyllite is a complex group of sorosilicates with general chemical formula given as A2B4C2Si2O7(X)4, where the site A can be occupied by strontium, barium, sodium, and potassium; the B site is occupied by sodium, titanium, iron, manganese, magnesium, and calcium. The site C is mainly occupied by titanium or ferric iron and X includes the anions fluoride, hydroxyl, and oxide. Chemical composition shows a homogeneous phase, composed of Si, Na, Ti, and Fe. This complexity of formula is reflected in the complexity of both the Raman and infrared spectra. The Raman spectrum is characterized by intense bands at 918 and 940 cm−1. Other intense Raman bands are found at 576, 671, and 707 cm−1. These bands are assigned to the stretching and bending modes of the tetrahedral siloxane units.

Characterization of epitopes for virus-neutralizing monoclonal antibodies to Ross River virus E2 using phage-displayed random peptide libraries

Ross River virus (RRV) is the predominant cause of epidemic polyarthritis in Australia, yet the antigenic determinants are not well defined. We aimed to characterize epitope(s) on RRV-E2 for a panel of monoclonal antibodies (MAbs) that recognize overlapping conformational epitopes on the E2 envelope protein of RRV and that neutralize virus infection of cells in vitro. Phage-displayed random peptide libraries were probed with the MAbs T1E7, NB3C4, and T10C9 using solution-phase and solid-phase biopanning methods. The peptides VSIFPPA and KTAISPT were selected 15 and 6 times, respectively, by all three of the MAbs using solution-phase biopanning. The peptide LRLPPAP was selected 8 times by NB3C4 using solid-phase biopanning; this peptide shares a trio of amino acids with the peptide VSIFPPA. Phage that expressed the peptides VSIFPPA and LRLPPAP were reactive with T1E7 and/or NB3C4, and phage that expressed the peptides VSIFPPA, LRLPPAP, and KTAISPT partially inhibited the reactivity of T1E7 with RRV. The selected peptides resemble regions of RRV-E2 adjacent to sites mutated in neutralization escape variants of RRV derived by culture in the presence of these MAbs (E2 210-219 and 238-245) and an additional region of E2 172-182. Together these sites represent a conformational epitope of E2 that is informative of cellular contact sites on RRV.

Growth and characterization of pure and doped single crystals of $CuGeO_{3}$

Good quality single crystals of copper metagermanite, CuGeO3, are grown by flux technique. Growth is carried out at relatively low temperatures by using Bi2O3 along with CuO in an optimal flux ratio. Besides rendering the procedure simple, lower growth temperature reduces growth defect concentration. Single crystals of Cu1 - xCoxGeO3 and CuGe1 - yGayO3 are grown by the same method for different values of x and y to investigate the influence of in-chain and off-chain doping on spin-Peierls (SP) transition. Change in color, morphology and surface features as a result of doping are briefly discussed. Spin-Peierls transition of these crystals is studied by susceptibility measurements on a commercial SQUID magnetometer. Cationic substitution resulted in reduction of spin-Peierls transition temperature (T-SP) of CuGeO3. Substitution of magnetic impurity cobalt in-chain site caused more pronounced effects such as suppression of SP phase.

Characterization of Ion-Exchange Fibers for Controlled Drug Delivery

Increasing attention has been focused on methods that deliver pharmacologically active compounds (e.g. drugs, peptides and proteins) in a controlled fashion, so that constant, sustained, site-specific or pulsatile action can be attained. Ion-exchange resins have been widely studied in medical and pharmaceutical applications, including controlled drug delivery, leading to commercialisation of some resin based formulations. Ion-exchangers provide an efficient means to adjust and control drug delivery, as the electrostatic interactions enable precise control of the ion-exchange process and, thus, a more uniform and accurate control of drug release compared to systems that are based only on physical interactions. Unlike the resins, only few studies have been reported on ion-exchange fibers in drug delivery. However, the ion-exchange fibers have many advantageous properties compared to the conventional ion-exchange resins, such as more efficient compound loading into and release from the ion-exchanger, easier incorporation of drug-sized compounds, enhanced control of the ion-exchange process, better mechanical, chemical and thermal stability, and good formulation properties, which make the fibers attractive materials for controlled drug delivery systems. In this study, the factors affecting the nature and strength of the binding/loading of drug-sized model compounds into the ion-exchange fibers was evaluated comprehensively and, moreover, the controllability of subsequent drug release/delivery from the fibers was assessed by modifying the conditions of external solutions. Also the feasibility of ion-exchange fibers for simultaneous delivery of two drugs in combination was studied by dual loading. Donnan theory and theoretical modelling were applied to gain mechanistic understanding on these factors. The experimental results imply that incorporation of model compounds into the ion-exchange fibers was attained mainly as a result of ionic bonding, with additional contribution of non-specific interactions. Increasing the ion-exchange capacity of the fiber or decreasing the valence of loaded compounds increased the molar loading, while more efficient release of the compounds was observed consistently at conditions where the valence or concentration of the extracting counter-ion was increased. Donnan theory was capable of fully interpreting the ion-exchange equilibria and the theoretical modelling supported precisely the experimental observations. The physico-chemical characteristics (lipophilicity, hydrogen bonding ability) of the model compounds and the framework of the fibrous ion-exchanger influenced the affinity of the drugs towards the fibers and may, thus, affect both drug loading and release. It was concluded that precisely controlled drug delivery may be tailored for each compound, in particularly, by choosing a suitable ion-exchange fiber and optimizing the delivery system to take into account the external conditions, also when delivering two drugs simultaneously.