Validation of the VE1 immunostain for the BRAF V600E mutation in melanoma

BACKGROUND: BRAF mutation status, and therefore eligibility for BRAF inhibitors, is currently determined by sequencing methods. We assessed the validity of VE1, a monoclonal antibody against the BRAF V600E mutant protein, in the detection of mutant BRAF V600E melanomas as classified by DNA pyrosequencing. METHODS: The cases were 76 metastatic melanoma patients with only one known primary melanoma who had had BRAF codon 600 pyrosequencing of either their primary (n = 19), metastatic (n = 57) melanoma, or both (n = 17). All melanomas (n = 93) were immunostained with the BRAF VE1 antibody using a red detection system. The staining intensity of these specimens was scored from 0 to 3+ by a dermatopathologist. Scores of 0 and 1+ were considered as negative staining while scores of 2+ and 3+ were considered positive. RESULTS: The VE1 antibody showed a sensitivity of 85% and a specificity of 100% as compared to DNA pyrosequencing results. There was 100% concordance between VE1 immunostaining of primary and metastatic melanomas from the same patient. V600K, V600Q, and V600R BRAF melanomas did not positively stain with VE1. CONCLUSIONS: This hospital-based study finds high sensitivity and specificity for the BRAF VE1 immunostain in comparison to pyrosequencing in detection of BRAF V600E in melanomas

IL2 Inducible T-cell Kinase, a Novel Therapeutic Target in Melanoma

Interleukin-2 inducible T-cell kinase (ITK) promoter CpG sites are hypomethylated in melanomas compared to nevi. The expression of ITK in melanomas, however, has not been established and requires elucidation

Simple scoring system to predict in-hospital mortality after surgery for infective endocarditis

BACKGROUND: Aspecific scoring systems are used to predict the risk of death postsurgery in patients with infective endocarditis (IE). The purpose of the present study was both to analyze the risk factors for in-hospital death, which complicates surgery for IE, and to create a mortality risk score based on the results of this analysis. METHODS AND RESULTS: Outcomes of 361 consecutive patients (mean age, 59.1\ub115.4 years) who had undergone surgery for IE in 8 European centers of cardiac surgery were recorded prospectively, and a risk factor analysis (multivariable logistic regression) for in-hospital death was performed. The discriminatory power of a new predictive scoring system was assessed with the receiver operating characteristic curve analysis. Score validation procedures were carried out. Fifty-six (15.5%) patients died postsurgery. BMI >27 kg/m2 (odds ratio [OR], 1.79; P=0.049), estimated glomerular filtration rate 55 mm Hg (OR, 1.78; P=0.032), and critical state (OR, 2.37; P=0.017) were independent predictors of in-hospital death. A scoring system was devised to predict in-hospital death postsurgery for IE (area under the receiver operating characteristic curve, 0.780; 95% CI, 0.734-0.822). The score performed better than 5 of 6 scoring systems for in-hospital death after cardiac surgery that were considered. CONCLUSIONS: A simple scoring system based on risk factors for in-hospital death was specifically created to predict mortality risk postsurgery in patients with IE

Molecular tools for the study of marine microbial diversity

Marine photosynthetic microbial organisms are the major, sustaining components of ecosystem processes and are responsible for biogeochemical reactions that drive our climate changes. Despite this, many marine microorganisms are poorly described and little is known of broad spatial and temporal scale trends in their abundance and distribution. With new molecular and analytical techniques we can advance our knowledge of marine biodiversity at the species level to understand how marine biodiversity supports ecosystem structure, dynamics and resilience. We can then interpret environmental, ecological and evolutionary processes controlling and structuring marine ecosystem biodiversity. With better analytical methods available, we can augment our understanding of biodiversity and ecosystem dynamics in especially the pico- and nano-fractions of the plankton as well as in the deep sea benthos, both of which are very difficult to study. Here we provide examples of new and long standing molecular tools for researchers in marine ecosystems to enable them to provide better, faster and more accurate estimates of marine biodiversity in the community using tools at the forefront of molecular research

Automated identification and characterisation of microbial populations using flow cytometry: the AIMS project

The AIMS (Automatic Identification and characterisation of Microbial populationS) project is developing and integrating flowcytometric technology for the identification of microbial cell populations and the determination of their cellular characteristics.This involves applying neural network approaches and molecular probes to the identification of cell populations, and derivingand verifying algorithms for assessing the chemical, optical and morphometric characteristics of these populations. The productsof AIMS will be calibrated data, protocols, algorithms and software designed to turn flow cytometric observations into a datamatrix of the abundance and cellular characteristics of identifiable populations. This paper describes the general approach of theAIMS project, with details on the application of artificial neural nets and rRNA oligonucleotide probes

Discrimination of the toxigenic dinoflagellate species Alexandrium tamarense and Alexandrium ostenfeldii in co-occurring natural populations from Scottish coastal waters

Blooms of the toxic dinoflagellate Alexandrium tamarense (Lebour) Balech, a known producer of potent neurotoxins associated with paralytic shellfish poisoning (PSP), are common annual events along the Scottish east coast. The co-occurrence of a second Alexandrium species, A. ostenfeldii (Paulsen) Balech & Tangen is reported in this study from waters of the Scottish east coast. The latter species has been suspected to be an alternative source of PSP toxins in northern Europe. Recent identification of toxic macrocyclic imines known as spirolides in A. ostenfeldii indicates a potential new challenge for monitoring toxic Alexandrium species and their respective toxins in natural populations. In mixed phytoplankton assemblages, Alexandrium species are dicult to discriminate accurately by conventional light microscopy. Species-specific rRNA probes based upon 18S and 28S ribosomal DNA sequences were developed for A. ostenfeldii and tested by dot-blot and fluorescence in situ hybridization (FISH) techniques. Hybridization patterns of A. ostenfeldii probes for cultured Alexandrium isolates, and cells from field populations from the Scottish east coast, were compared with those of rDNA probes for A. tamarense and a universal dinoflagellate probe. Alexandrium cell numbers in field samples determined by whole-cell in situ hybridization were much lower than those determined by optical microscopy with the Utermöhl method involving sedimentation chambers, but the results were highly correlated (e.g. r2=0.94; n=6 for A. tamarense). Determination of spirolides and PSP toxins by instrumental analysis on board ship demonstrated the presence of both toxi

Inherited variation at MC1R and histological characteristics of primary melanoma.

Variation in the melanocortin-1receptor (MC1R) gene is associated with pigmentary phenotypes and risk of malignant melanoma. Few studies have reported on MC1R variation with respect to tumor characteristics, especially clinically important prognostic features. We examined associations between MC1R variants and histopathological melanoma characteristics. Study participants were enrolled from nine geographic regions in Australia, Canada, Italy and the United States and were genotyped for MC1R variants classified as high-risk [R] (D84E, R142H, R151C, R160W, and D294H, all nonsense and insertion/deletion) or low-risk [r] (all other nonsynonymous) variants. Tissue was available for 2,160 white participants of the Genes, Environment and Melanoma (GEM) Study with a first incident primary melanoma diagnosis, and underwent centralized pathologic review. No statistically significant associations were observed between MC1R variants and AJCC established prognostic tumor characteristics: Breslow thickness, presence of mitoses or presence of ulceration. However, MC1R was significantly associated with anatomic site of melanoma (p = 0.002) and a positive association was observed between carriage of more than one [R] variant and melanomas arising on the arms (OR = 2.39; 95% CI: 1.40, 4.09). We also observed statistically significant differences between sun-sensitive and sun-resistant individuals with respect to associations between MC1R genotype and AJCC prognostic tumor characteristics. Our results suggest inherited variation in MC1R may play an influential role in anatomic site presentation of melanomas and may differ with respect to skin pigmentation phenotype