Genomic deletions at 1p and 14q are associated with an abnormal cDNA microarray gene expression pattern in meningiomas but not in schwannomas

The molecular pathology of meningiomas and shwannomas involve the inactivation of the NF2 gene to generate grade I tumors. Genomic losses at 1p and 14q are observed in both neoplasms, although more frequently in meningiomas. The inactivation of unidentified genes located in these regions appears associated with tumor progression in meningiomas, but no clues to its molecular/clinical meaning are available in schwannomas. Recent microarray gene expression studies have demonstrated the existence of molecular subgroups in both entities. In the present study, we correlated the presence of genomic deletions at 1p, 14q, and 22q with the expression patterns of 96 tumor-related genes obtained by cDNA low-density microarrays in a series of 65 tumors including 42 meningiomas and 23 schwannomas. Two expression pattern groups were identified by cDNA mycroarray analysis when compared to the expression pattern in normal control RNA in both meningiomas and schwannomas, each one with patterns similar and different from the normal control. Meningioma and schwannoma subgroups differed in the expression of 38 and 16 genes, respectively. Using MLPA and microsatellites, we identified genomic losses at 1p, 14q, and 22q at nonrandom frequencies (12.5-69%) in meningiomas and schwannomas. Losses at 22q were almost equally frequent in both molecular expression subgroups in both neoplasms. However, deletions at 1p and 14q accumulated in meningiomas with a gene expression pattern different from the normal pattern, whereas the inverse situation occurred in schwannomas. Those anomalies characterized the schwannomas with expression pattern similar to the normal control. These findings suggest that deletions at 1p and 14q enhance the development of an abnormal tumor-related gene expression pattern in meningiomas, but this fact is not corroborated in schwannomas. (C) 2010 Elsevier Inc. All rights reserved.

Comparison of the Use of Tympanic and Extratympanic Electrodes for Electrocochleography

Objectives: To determine the differences between tympanic and extratympanic electrodes regarding recording technique, comfort and ease of execution of the exam, and quality of auditory potential tracings. Study Design: Prospective cross-section investigation. Methods: Determination of the summation potential/action potential (SP/AP) ratio by electrocochleography (EchoG) using tympanic and extratympanic electrodes and separate analysis of SP and AP regarding the amplitude recorded. Results: Twenty-three subjects (15 men and 8 women; mean age: 33.17 years) with normal tonal threshold audiometry were evaluated. EchoG analysis revealed no significant difference between the two tympanic electrodes. Eleven of the 23 subjects reported discomfort with the insertion of the tympanic electrode even with the use of topical xylocaine, whereas no complaints of discomfort were reported with the use of the extratympanic electrode. Conclusions: Both electrodes were effective for EchoG evaluation, but the extratympanic one was easier to insert and did not cause discomfort. However, the tympanic electrode produced tracings of greater amplitude and of better reproducibility. Laryngoscope, 119:563-566, 2009

Loss of samples in the tissue microarray technique: comparison between slides using adhesive tape and silanized slides

The tissue microarray (TMA) technique allows multiple tissue samples in a single block. Commercial adhesive tape is used to avoid the loss of tissue samples during the immunostaining process. Few reports exist in the literature comparing the use of these adhesive tapes to other adhesive techniques. The objective of this study was to compare loss of sections adhered to slides using commercial adhesive tapes versus using silanized only slides. TMA was constructed with varying tissues using a fixed-base device (Beecher Instruments), placing 108 cylinders of 1 mm diameter in duplicate, spaced 1.2 mm apart. Section of 4 mu m were cut from the TMA block and adhered to 30 silanized slides and 30 commercial glass slides using adhesive tape, according to manufacturer`s recommendations. Vimentin immunoexpression was evaluated by immunohistochemistry. Antigenic recovery was realized in citrate buffer using a microwave oven. Cylinder loss in the immunohistochemical process was quantified and expressed as: total (>80%), almost complete (75-79%), or partial (50-74%). The commercial adhesive tape group presented lesser total loss (1.1 versus 6.4%), almost complete loss (2.2 versus 3.5%), and partial loss (2.1 versus 3.8%) than the silanized slide group (ANOVA, P < 0.05). The sum of total and almost complete losses in the silanized slide group was 9.9%, greater than the losses in slides using commercial adhesive tapes (3.3%) and less than reported and considered acceptable in the literature (10-30%). In conclusion, the use of silanized only slides presents very satisfactory results, requires less training, and reduces costs significantly, thus justifying their use in research.

Nucleophosmin, p53, and Ki-67 expression patterns on an oral squamous cell carcinoma tissue microarray

Oral cancer is the eighth most prevalent cancer worldwide. It causes significant mortality and morbidity rates, which have motivated the search for prognostic factors to better tailor the individual management of oral squamous cell carcinoma patients. Nucleophosmin is a multifunctional protein that is involved in many cellular activities, such as, regulation of the tumor suppressor genes TP53 and p14(ARF). and is associated with proliferative and growth suppressive roles in the cell. Nucleophosmin is overexpressed in many solid tumors in human, including tumors of the colon, liver, stomach, ovary, and prostate. In this study, we analyzed the expression of nucleophosmin, Ki-67, and p53 by immunohistochemistry in oral squamous cell carcinomas. Less than 10% of nuclear staining was observed in 90.3%, 50.6%, and 65.3% of the cases for nucleophosmin, p53, and Ki-67, respectively. Expression of p53 was not significantly associated with any of the clinicopathologic parameters analyzed. Increased expression of Ki-67 was associated with the presence of lymph node metastasis (P < .0001), advanced stages of disease (P = .0030), tumors occurring in the floor of mouth (P = .0018), and moderately/well-differentiated tumors (P = .0287). Local recurrence was associated with higher expression of nucleophosmin (P = .0233), and disease-free survival rate was significantly better in patients with low expression of nucleophosmin. Multivariate analysis suggested that expression of nucleophosmin could be an independent prognostic factor for oral squamous cell carcinoma patients. (C) 2010 Elsevier Inc. All rights reserved.

Oral squamous cell carcinoma: status of tight junction claudins in the different histopathological patterns and relationship with clinical parameters. A tissue-microarray-based study of 136 cases

Aims Claudins are integral transmembrane proteins of the tight junctions, critical for maintaining cell adhesion and polarity. Alterations in the expression of individual claudins have been detected in carcinomas and appear to correlate with tumour progression. Methods In this study, a panel of anti-claudin antibodies (anti-claudins 1, 2, 3, 4, 5 and 7) was employed to map claudin expression in 136 cases of oral squamous cell carcinoma (OSCC) organised in a tissue microarray. Results Claudins were expressed in a reticular pattern up to the prickle layer in normal mucosal epithelium. In OSCC, claudins were strongly present in well-differentiated tumours, they presented mild and low expression in moderately differentiated OSCC, and were negative in poorly differentiated OSCC; the absences of claudin 1 (p = 0.002) and claudin 4 (p<0.001) were associated with moderately/poorly differentiated tumours. Strong expression of claudin 4 was associated with decreased perineural infiltration (p = 0.024). Claudins 5 and 7 were mostly negative or weakly expressed in all cases studied. Expression of claudin 7 was associated with the early clinical stages of the disease, whereas loss of claudin 7 tended to be more frequent in advanced stages of OSCC (p = 0.054). Absence of claudin 7 was also associated with absent vascular infiltration (p = 0.045) and with presence of recurrence (p = 0.052). Conclusions Claudin expression patterns showed a strong correlation with histological type of OSCC; claudin expression was decreased in areas of invasion, and negative in poorly differentiated tumours. This pattern may be related to evolution and prognosis of these tumours, especially in the case of claudin 7, which seems to be associated with a poor prognosis in OSCC.

A mixture model-based approach to the clustering of microarray expression data

Motivation: This paper introduces the software EMMIX-GENE that has been developed for the specific purpose of a model-based approach to the clustering of microarray expression data, in particular, of tissue samples on a very large number of genes. The latter is a nonstandard problem in parametric cluster analysis because the dimension of the feature space (the number of genes) is typically much greater than the number of tissues. A feasible approach is provided by first selecting a subset of the genes relevant for the clustering of the tissue samples by fitting mixtures of t distributions to rank the genes in order of increasing size of the likelihood ratio statistic for the test of one versus two components in the mixture model. The imposition of a threshold on the likelihood ratio statistic used in conjunction with a threshold on the size of a cluster allows the selection of a relevant set of genes. However, even this reduced set of genes will usually be too large for a normal mixture model to be fitted directly to the tissues, and so the use of mixtures of factor analyzers is exploited to reduce effectively the dimension of the feature space of genes. Results: The usefulness of the EMMIX-GENE approach for the clustering of tissue samples is demonstrated on two well-known data sets on colon and leukaemia tissues. For both data sets, relevant subsets of the genes are able to be selected that reveal interesting clusterings of the tissues that are either consistent with the external classification of the tissues or with background and biological knowledge of these sets.

Celiac disease detection using a transglutaminase electrochemical immunosensor fabricated on nanohybrid screen-printed carbon electrodes

Celiac disease is a gluten-induced autoimmune enteropathy characterized by the presence of tissue tranglutaminase (tTG) autoantibodies. A disposable electrochemical immunosensor (EI) for the detection of IgA and IgG type anti-tTG autoantibodies in real patient’s samples is presented. Screen-printed carbon electrodes (SPCE) nanostructurized with carbon nanotubes and gold nanoparticles were used as the transducer surface. This transducer exhibits the excellent characteristics of carbon–metal nanoparticle hybrid conjugation and led to the amplification of the immunological interaction. The immunosensing strategy consisted of the immobilization of tTG on the nanostructured electrode surface followed by the electrochemical detection of the autoantibodies present in the samples using an alkaline phosphatase (AP) labelled anti-human IgA or IgG antibody. The analytical signal was based on the anodic redissolution of enzymatically generated silver by cyclic voltammetry. The results obtained were corroborated with a commercial ELISA kit indicating that the electrochemical immunosensor is a trustful analytical screening tool.

Electrodeposition and characterization of nickel–copper metallic foams for application as electrodes for supercapacitors

Nickel-copper metallic foams were electrodeposited from an acidic electrolyte, using hydrogen bubble evolution as a dynamic template. Their morphology and chemical composition was studied by scanning electron microscopy and related to the deposition parameters (applied current density and deposition time). For high currents densities (above 1 A cm(-2)) the nickel-copper deposits have a three-dimensional foam-like morphology with randomly distributed nearly-circular pores whose walls present an open dendritic structure. The nickel-copper foams are crystalline and composed of pure nickel and a copper-rich phase containing nickel in solid solution. The electrochemical behaviour of the material was studied by cyclic voltammetry and chronopotentiometry (charge-discharge curves) aiming at its application as a positive electrode for supercapacitors. Cyclic voltammograms showed that the Ni-Cu foams have a pseudocapacitive behaviour. The specific capacitance was calculated from charge-discharge data and the best value (105 F g(-1) at 1 mA cm(-2)) was obtained for nickel-copper foams deposited at 1.8 A cm(-2) for 180 s. Cycling stability of these foams was also assessed and they present a 90 % capacitance retention after 10,000 cycles at 10 mA cm(-2).

Arrow plot and CA maps on microarray preprocessing methods

Microarray allow to monitoring simultaneously thousands of genes, where the abundance of the transcripts under a same experimental condition at the same time can be quantified. Among various available array technologies, double channel cDNA microarray experiments have arisen in numerous technical protocols associated to genomic studies, which is the focus of this work. Microarray experiments involve many steps and each one can affect the quality of raw data. Background correction and normalization are preprocessing techniques to clean and correct the raw data when undesirable fluctuations arise from technical factors. Several recent studies showed that there is no preprocessing strategy that outperforms others in all circumstances and thus it seems difficult to provide general recommendations. In this work, it is proposed to use exploratory techniques to visualize the effects of preprocessing methods on statistical analysis of cancer two-channel microarray data sets, where the cancer types (classes) are known. For selecting differential expressed genes the arrow plot was used and the graph of profiles resultant from the correspondence analysis for visualizing the results. It was used 6 background methods and 6 normalization methods, performing 36 pre-processing methods and it was analyzed in a published cDNA microarray database (Liver) available at http://genome-www5.stanford.edu/ which microarrays were already classified by cancer type. All statistical analyses were performed using the R statistical software.

Determination of tartaric acid in wines by FIA with tubular tartrate-selective electrodes

A flow injection analysis (FIA) system comprising a tartrate- (TAT) selective electrode has been developed for determination of tartaric acid in wines. Several electrodes constructed for this purpose had a PVC membrane with a complex of quaternary ammonium and TAT as anion exchanger, a phenol derivative as additive, and a more or less polar mediator solvent. Characterization of the electrodes showed behavior was best for membranes with o-nitrophenyl octyl ether as solvent. On injection of 500 μL into a phosphate buffer carrier (pH = 3.1; ionic strength 10–2 mol/L) flowing at 3 mL/min, the slope was 58.06 ± 0.6 with a lower limit of linear range of 5.0 × 10–4 mol/L TAT and R2 = 0.9989. The interference of several species, e.g. chloride, bromide, iodide, nitrate, gallic acid, tannin, sucrose, glucose, fructose, acetate, and citrate, was evaluated in terms of potentiometric selectivity coefficients. The Hofmeister series was followed for inorganic species and the most interfering organic ion was citrate. When red and white wines were analyzed and the results compared with those from an independent method they were found to be accurate, with relative standard deviations below 5.0%.

Citrate selective electrodes for the flow injection analysis of soft drinks, beers and pharmaceutical products

Aiming the establishment of simple and accurate readings of citric acid (CA) in complex samples, citrate (CIT) selective electrodes with tubular configuration and polymeric membranes plus a quaternary ammonium ion exchanger were constructed. Several selective membranes were prepared for this purpose, having distinct mediator solvents (with quite different polarities) and, in some cases, p-tert-octylphenol (TOP) as additive. The latter was used regarding a possible increase in selectivity. The general working characteristics of all prepared electrodes were evaluated in a low dispersion flow injection analysis (FIA) manifold by injecting 500µl of citrate standard solutions into an ionic strength (IS) adjuster carrier (10−2 mol l−1) flowing at 3ml min−1. Good potentiometric response, with an average slope and a repeatability of 61.9mV per decade and ±0.8%, respectively, resulted from selective membranes comprising additive and bis(2-ethylhexyl)sebacate (bEHS) as mediator solvent. The same membranes conducted as well to the best selectivity characteristics, assessed by the separated solutions method and for several chemical species, such as chloride, nitrate, ascorbate, glucose, fructose and sucrose. Pharmaceutical preparations, soft drinks and beers were analyzed under conditions that enabled simultaneous pH and ionic strength adjustment (pH = 3.2; ionic strength = 10−2 mol l−1), and the attained results agreed well with the used reference method (relative error < 4%). The above experimental conditions promoted a significant increase in sensitivity of the potentiometric response, with a supra-Nernstian slope of 80.2mV per decade, and allowed the analysis of about 90 samples per hour, with a relative standard deviation <1.0%.

Construction and evaluation of cysteine selective electrodes for FIA analysis of pharmaceuticals

A flow injection analysis (FIA) system comprising a cysteine selective electrode as detection system was developed for determination of this amino acid in pharmaceuticals. Several electrodes were constructed for this purpose, having PVC membranes with different ionic exchangers and mediator solvents. Better working characteristics were attained with membranes comprising o-nitrophenyl octyl ether as mediator solvent and a tetraphenylborate based ionic-sensor. Injection of 500 µL standard solutions into an ionic strength adjuster carrier (3x10-3 M) of barium chloride flowing at 2.4mL min-1, showed linearity ranges from 5.0x10-5 to 5.0x10-3 M, with slopes of 76.4±0.6mV decade-1 and R2>0.9935. Slope decreased significantly under the requirement of a pH adjustment, selected at 4.5. Interference of several compounds (sodium, potassium, magnesium, barium, glucose, fructose, and sucrose) was estimated by potentiometric selectivity coefficients and considered negligible. Analysis of real samples were performed and considered accurate, with a relative error to an independent method of +2.7%.

Chlormequat selective electrodes: construction, evaluation and application at FIA systems

A flow injection analysis (FIA) system having a chlormequat selective electrode is proposed. Several electrodes with poly(vinyl chloride) based membranes were constructed for this purpose. Comparative characterization suggestedthe use of membrane with chlormequat tetraphenylborate and dibutylphthalate. On a single-line FIA set-up, operating with 1x10-2 mol L-1 ionic strength and 6.3 pH, calibration curves presented slopes of 53.6±0.4mV decade-1 within 5.0x10-6 and1.0x10-3 mol L-1, andsquaredcorrelation coefficients >0.9953. The detection limit was 2.2x10-6 mol L-1 and the repeatability equal to ±0.68mV (0.7%). A dual-channel FIA manifold was therefore constructed, enabling automatic attainment of previous ionic strength andpH conditions and thus eliminating sample preparation steps. Slopes of 45.5±0.2mV decade -1 along a concentration range of 8.0x10-6 to 1.0x10-3 mol L-1 with a repeatability ±0.4mV (0.69%) were obtained. Analyses of real samples were performed, and recovery gave results ranging from 96.6 to 101.1%.

Trimethoprim-selective electrodes with molecularly imprinted polymers acting as ionophores and potentiometric transduction on graphite solid-contact

This work proposes a new biomimetic sensor material for trimethoprim. It is prepared by means of radical polymerization, having trimethylolpropane trimethacrylate as cross-linker, benzoyl peroxide as radicalar iniciator, chloroform as porogenic solvent, and methacrylic acid and 2-vinyl pyridine as monomers. Different percentages of sensor in a range between 1 and 6% were studied. Their behavior was compared to that obtained with ion-exchanger quaternary ammonium salt (additive tetrakis(p-chlorophenyl)borate or tetraphenylborate). The effect of an anionic additive in the sensing membrane was also tested. Trimethoprim sensors with 1% of imprinted particles from methacrylic acid monomers showed the best response in terms of slope (59.7 mV/decade) and detection limit (4.01×10−7 mol/L). These electrodes displayed also a good selectivity towards nickel, manganese aluminium, ammonium, lead, potassium, sodium, iron, chromium, sulfadiazine, alanine, cysteine, tryptophan, valine and glycine. The sensors were not affected by pH changes from 2 to 6. They were successfully applied to the analysis of water from aquaculture.