An integrated genomic analysis of human glioblastoma Multiforme

Glioblastoma multiforme ( GBM) is the most common and lethal type of brain cancer. To identify the genetic alterations in GBMs, we sequenced 20,661 protein coding genes, determined the presence of amplifications and deletions using high- density oligonucleotide arrays, and performed gene expression analyses using next- generation sequencing technologies in 22 human tumor samples. This comprehensive analysis led to the discovery of a variety of genes that were not known to be altered in GBMs. Most notably, we found recurrent mutations in the active site of isocitrate dehydrogenase 1 ( IDH1) in 12% of GBM patients. Mutations in IDH1 occurred in a large fraction of young patients and in most patients with secondary GBMs and were associated with an increase in overall survival. These studies demonstrate the value of unbiased genomic analyses in the characterization of human brain cancer and identify a potentially useful genetic alteration for the classification and targeted therapy of GBMs.

The Genetic Landscape of the Childhood Cancer Medulloblastoma

Medulloblastoma (MB) is the most common malignant brain tumor of children. To identify the genetic alterations in this tumor type, we searched for copy number alterations using high-density microarrays and sequenced all known protein-coding genes and microRNA genes using Sanger sequencing in a set of 22 MBs. We found that, on average, each tumor had 11 gene alterations, fewer by a factor of 5 to 10 than in the adult solid tumors that have been sequenced to date. In addition to alterations in the Hedgehog and Wnt pathways, our analysis led to the discovery of genes not previously known to be altered in MBs. Most notably, inactivating mutations of the histone-lysine N-methyltransferase genes MLL2 or MLL3 were identified in 16% of MB patients. These results demonstrate key differences between the genetic landscapes of adult and childhood cancers, highlight dysregulation of developmental pathways as an important mechanism underlying MBs, and identify a role for a specific type of histone methylation in human tumorigenesis.

Do Phenotypic Characteristics, Parental Psychopathology, Family Functioning, and Environmental Stressors Have a Role in the Response to Methylphenidate in Children With Attention-Deficit/Hyperactivity Disorder? A Naturalistic Study From a Developing Country

Little is known about the effect of clinical characteristics, parental psychopathology, family functioning, and environmental stressors in the response to methylphenidate in children with attention-deficit/hyperactivity disorder (ADHD) followed up in a naturalistic setting. Data from cultures outside the United States are extremely scarce. This is a longitudinal study using a nonrandom assignment, quasi-experimental design. One hundred twenty-five children with ADHD were treated with methylphenidate according to standard clinical procedures, and followed up for 6 months. The severity of ADHD symptoms was assessed by the Swanson, Nolan, and Pelham rating scale. In the final multivariate model, ADHD combined subtype (P < 0.001) and comorbidity with oppositional defiant disorder (P = 0.03) were both predictors of a worse clinical response. In addition, the levels of maternal ADHD symptoms were also associated with worse prognosis (P < 0.001). In the context of several adverse psychosocial factors assessed, only undesired pregnancy was associated with poorer response to methylphenidate in the final comprehensive-model (P = 0.02). Our study provides evidence for the involvement of clinical characteristics, maternal psychopathology, and environmental stressors in the response to methylphenidate. Clinicians may consider adjuvant strategies when negative predictors are present to increase the chances of success with methylphenidate treatment.

Annexin A1 subcellular expression in laryngeal squamous cell carcinoma

Annexin A1 (ANXA1) is a soluble cytoplasmic protein, moving to membranes when calcium levels are elevated. ANXA1 has also been shown to move to the nucleus or outside the cells, depending on tyrosine-kinase signalling, thus interfering in cytoskeletal organization and cell differentiation, mostly in inflammatory and neoplastic processes. The aim was to investigate subcellular patterns of immunohistochemical expression of ANXA1 in neoplastic and non-neoplastic samples from patients with laryngeal squamous cell carcinomas (LSCC), to elucidate the role of ANXA1 in laryngeal carcinogenesis. Serial analysis of gene expression experiments detected reduced expression of ANXA1 gene in LSCC compared with the corresponding non-neoplastic margins. Quantitative polymerase chain reaction confirmed ANXA1 low expression in 15 LSCC and eight matched normal samples. Thus, we investigated subcellular patterns of immunohistochemical expression of ANXA1 in 241 paraffin-embedded samples from 95 patients with LSCC. The results showed ANXA1 down-regulation in dysplastic, tumourous and metastatic lesions and provided evidence for the progressive migration of ANXA1 from the nucleus towards the membrane during laryngeal tumorigenesis. ANXA1 dysregulation was observed early in laryngeal carcinogenesis, in intra-epithelial neoplasms; it was not found related to prognostic parameters, such as nodal metastases.

Epstein-Barr virus detection in invasive and pre-invasive lesions of the uterine cervix

In the present study, our aim was to investigate whether EBV DNA could be found in association with invasive and pre-invasive cervical cancer lesions. We hypothesize that EBV is not merely a commensal agent when present in malignant cervical lesions. DNA was extracted from cervical scrapings followed by nested PCR-based amplification. The patients were 66 women with high grade cervical intraepithelial neoplasia and 14 women with invasive cervical cancer. The control group consisted of 89 women with a normal Pap smear and colposcopy as well as a negative HPV DNA test. Analysis of our results, in conjunction with the work of other authors, leads us to propose that EBV is not merely a commensal agent when present in malignant cervical lesions. The presence of DNA from EBV is significantly associated with cervical cancer.

Association of EGFR c.2073A > T polymorphism with decreased risk of diffusely infiltrating astrocytoma in a Brazilian case-control study

Epidermal growth factor receptor (EGFR) gene overexpression has been implicated in the development of many types of tumors, including glioblastomas, the most frequent diffusely infiltrating astrocytomas. However, little is known about the influence of the polymorphisms of EGFR on EGFR production and/or activity, possibly modulating the susceptibility to astrocytomas. This study aimed to examine the association of two EGFR promoter polymorphisms (c.-191C > A and c.-216G > T) and the c.2073A > T polymorphism located in exon 16 with susceptibility to astrocytomas, EGFR gene expression and survival in a case-control study of 193 astrocytoma patients and 200 cancer-free controls. We found that the variant TT genotype of the EGFR c.2073A > T polymorphism was associated with a significantly decreased risk of astrocytoma when compared with the AA genotype [sex- and age-adjusted odds ratio 0.51, 95% confidence interval 0.26-0.98]. No association of the two promoter EGFR polymorphisms (or combinations of these polymorphisms) and risk of astrocytomas, EGFR expression or survival was found. Our findings suggest that modulation of the EGFR c.2073A > T polymorphism could play a role in future therapeutic approaches to astrocytoma. (Int J Biol Markers 2008; 23: 140-6)

Distinct patterns of somatic alterations in a lymphoblastoid and a tumor genome derived from the same individual

Although patterns of somatic alterations have been reported for tumor genomes, little is known on how they compare with alterations present in non-tumor genomes. A comparison of the two would be crucial to better characterize the genetic alterations driving tumorigenesis. We sequenced the genomes of a lymphoblastoid (HCC1954BL) and a breast tumor (HCC1954) cell line derived from the same patient and compared the somatic alterations present in both. The lymphoblastoid genome presents a comparable number and similar spectrum of nucleotide substitutions to that found in the tumor genome. However, a significant difference in the ratio of non-synonymous to synonymous substitutions was observed between both genomes (P = 0.031). Protein-protein interaction analysis revealed that mutations in the tumor genome preferentially affect hub-genes (P = 0.0017) and are co-selected to present synergistic functions (P < 0.0001). KEGG analysis showed that in the tumor genome most mutated genes were organized into signaling pathways related to tumorigenesis. No such organization or synergy was observed in the lymphoblastoid genome. Our results indicate that endogenous mutagens and replication errors can generate the overall number of mutations required to drive tumorigenesis and that it is the combination rather than the frequency of mutations that is crucial to complete tumorigenic transformation.

Proteomic analysis of low- to high-grade astrocytomas reveals an alteration of the expression level of raf kinase inhibitor protein and nucleophosmin

Proteomic approaches have been useful for the identification of aberrantly expressed proteins in complex diseases such as cancer. These proteins are not only potential disease biomarkers, but also targets for therapy. The aim of this study was to identify differentially expressed proteins in diffuse astrocytoma grade II, anaplastic astrocytoma grade III and glioblastoma multiforme grade IV in human tumor samples and in non-neoplastic brain tissue as control using 2-DE and MS. Tumor and control brain tissue dissection was guided by histological hematoxylin/eosin tissue sections to provide more than 90% of tumor cells and astrocytes. Six proteins were detected as up-regulated in higher grade astrocytomas and the most important finding was nucleophosmin (NPM) (p < 0.05), whereas four proteins were down-regulated, among them raf kinase inhibitor protein (RKIP) (p < 0.05). We report here for the first time the alteration of NPM and RKIP expression in brain cancer. Our focus on these proteins was due to the fact that they are involved in the PI3K/AKT/mTOR and RAS/RAF/MAPK pathways, known for their contribution to the development and progression of gliomas. The proteomic data for NPM and RKIP were confirmed by Western blot, quantitative real-time PCR and immunohistochemistry. Due to the participation of NPM and RKIP in uncontrolled proliferation and evasion of apoptosis, these proteins are likely targets for drug development.

Dinoflagellate symbiosis: strategies and adaptations for the aquisition and fixation of inorganic carbon

Dinoflagellates exist in symbiosis with a number of marine invertebrates including giant clams, which are the largest of these symbiotic organisms. The dinoflagellates (Symbiodinium sp.) live intercellularly within tubules in the mantle of the host clam. The transport of inorganic carbon (Ci) from seawater to Symbiodinium (=zooxanthellae) is an essential function of hosts that derive the majority of their respiratory energy from the photosynthate exported by the zooxanthellae. Immunolocalisation studies show that the host has adapted its physiology to acquire, rather than remove CO2, from the haemolymph and clam tissues. Two carbonic anhydrase (CA) isoforms (32 and 70 kDa) play an essential part in this process. These have been localised to the mantle and gill tissues where they catalyse the interconversion of HCO3- to CO2, which then diffuses into the host tissues. The zooxanthellae exhibit a number of strategies to maximise Ci acquisition and utilisation. This is necessary as they express a form II Rubisco that has poor discrimination between CO2 and O-2. Evidence is presented for a carbon concentrating mechanism (CCM) to overcome. this disadvantage. The CCM incorporates the presence of a light-activated CA activity, a capacity to take up both HCO3- and CO2, an ability to accumulate an elevated concentration of Ci within the algal cell, and localisation of Rubisco to the pyrenoid. These algae also express both external and intracellular CAs, with the intracellular isoforms being localised to the thylakoid lumen and pyrenoid. These results have been incorporated into a model that explains the transport of Ci from seawater through the clam to the zooxanthellae.

Populações de plantas na cultura da soja em cultivares convencionais e Roundup ReadyTM

Este trabalho teve como objetivo estudar o comportamento de cultivares de soja convencionais e Roundup ReadyTM (RR) quando cultivados com diferentes populações de plantas por hectare. Foram realizados três ensaios no município de Jari, RS: em novembro de 2004 e de 2005 e em janeiro de 2006 (semeadura após a época indicada). Os cultivares convencionais utilizados foram: CEP/CD 41, CD 201, FUNDACEP 39 e CD 205 e os Roundup ReadyTM AL72, NK Mágica 7.3 RR e A 6001 RG nas populações de 250, 400 e 550 mil plantas ha-1. Em cada ensaio, o delineamento experimental utilizado foi blocos ao acaso, com 21 tratamentos e quatro repetições. Os tratamentos foram dispostos em esquema de parcelas subdivididas, representados pelos cultivares nas parcelas e pelas populações de plantas nas subparcelas. Foram avaliados a produtividade de grãos e os componentes da produção: legumes por planta e por m², peso de 100 grãos e número de grãos por legume. O comportamento dos cultivares convencionais e Roundup ReadyTM diferiu com a população de plantas. Em condição de estresse hídrico severo o aumento da população de plantas não afetou a produtividade. Somente o cultivar A 6001 RG apresentou rendimento estável nas diferentes populações de plantas, indicando que ele possui maior plasticidade. O número de legumes por planta foi reduzido com o aumento do número de plantas por área. As maiores produtividades foram alcançadas onde foi constatado maior número de legumes por m². O maior valor do peso de 100 grãos foi encontrado na maior população de plantas. O número de grãos por legume reduziu-se com o aumento da população de plantas. Condições de cultivo mais favoráveis tendem a aumentar o número de legumes/m², peso de 100 sementes e número de grãos por legume.

O piano (bem) informado : processos de interiorização e crescimento

Este livro debruça-se sobre questões ligadas à metodologia do piano, incluindo aspectos técnicos, musicais e artísticos, num enquadramento que engloba algumas das principais reflexões éticas, estéticas e filosóficas de referência. O objetivo deste trabalho é a partilha de uma visão baseada na experiência pessoal e profissional na área do piano. Este texto assume uma certa continuidade com as grandes contribuições de autores tais como Ludwig Deppe, Matthay Tobias, Grigory Kogan, Heinrich Neuhaus e George Kochevitsky publicado. Ao mesmo tempo que se integra e complementa alguma dessa literatura especializada, aponta ideias, sugestões e pontos de vista caracterizados pela inovação e aplicabilidade racional e científica.

The (well) informed piano : internalization and growth process

The subject matter of this book is about piano methodology, including technical, musical, artistic, ethical and philosophical issues and reflections. The purpose of this work is to share a personal professional experience insight in the field of piano performance. This text assumes a certain continuity to the major contributions of artists like Ludwig Deppe, Tobias Matthay, Grigory Kogan, Heinrich Neuhaus and George Kochevitsky. At the same time, it tries to integrate and complement this selected literature, bringing new ideas and hints to specific professional issues.

A Tradução reinventada em The Invention of Solitude de Paul Auster

A leitura da obra de Paul Auster, desde os primeiros poemas e ensaios até à mais recente ficção, revela uma constante reflexão metalinguística e metaficcional sobre o trabalho da escrita. Auster equaciona o problema da escrita enquanto acto, permitindo ao leitor acompanhar e participar desse processo de construção. A narrativa e a linguagem intelectualizam-se, tornam-se conscientes, o que possibilita uma aproximação privilegiada ao ensino da tradução de textos literários através da própria literatura. The Invention of Solitude é como uma arte poética inspirada na experiência efectiva do sujeito, enquanto escritor e tradutor. Podemos considerá-lo um romance-manifesto em duas partes (Portrait of an Invisible Man e The Book of Memory), com especial incidência na exploração analítica da cena da escrita, utilizando a personagem-escritor e suas vivências como cobaia neste processo de auto e heteroconhecimento. A partir da análise aplicada de The Invention of Solitude, este artigo irá remeter também para os ensaios de Ernest Gellner sobre Wittgenstein em Language and Solitude, entre outros escritores que se debruçaram igualmente sobre questões ligadas à tradução literária, como Dryden, Goethe, Nietzsche, Benjamin, Ortega y Gasset e Octávio Paz.

Feyerabend

É objectivo desta dissertação sobre Teoria e Incomensurabilidade em Feyerabend, aprofundar o conhecimento da problemática, da interpretação de teorias científicas e o contexto da sua emergência e configuração, tal como é dada a ler nos primeiros ensaios. Consideraram-se para o efeito, relevantes, sobretudo, as fontes primárias, em que tal temática é avaliada. O primeiro capítulo estrutura-se a partir de Realism and Historicity of Knowledge, escrito a pensar em Bohr, porque este ensaio, embora posterior, sintetiza os problemas que se levantam às tradições abstractas quando procuram acomodar o progresso científico, esquecendo a história. Assinalámos assim o fundo de tensão de que emerge o problema da avaliação do potencial heurístico das teorias científicas. Mobilizámos Knowledge without Foundations, por parecer incontornável a matriz popperiana da recusa fundacionalista que nesse período projectava, e Wittgenstein's Philosophical Investigations por levantar os problemas da pragmática do saber científico a partir da discussão dos jogos de linguagem e dos seus lances, porque os considerámos estruturantes. No segundo capítulo procurámos desenvolver o tema da incomensurabilidade entre teorias não instanciais sucessivas mobilizando para o efeito os ensaios onde nos pareceu ser dominante a análise e a perspectivação histórica do debate dialéctico (positivismo/realismo) acerca dos problemas decorrentes das interacções entre teoria e experiência, teoria e observação, teoria e linguagem corrente e teoria e prática científica como é o caso em Attempt at a Realistic Interpretation of Experience, em que avança a Tese I e expõe o irrealismo da tese da estabilidade e a irrelevância das mudanças no emprego de termos científicos na linguagem corrente, por força de mutações ocorridas na supra estrutura teórica. Desenvolvemos também a partir de Explanation, Reduction and Empiricism, os problemas e as dificuldades da interpretação de teorias científicas decorrentes da pretensão ortodoxa de justificação formal de redução e explicação de teorias gerais, desenvolvida quer na teoria da redução de Nagel, quer na teoria da explicação de Hempel e Oppenheim . Encerramos o capítulo com o problemas da testabilidade de teorias científicas e a solução que a adopção, quer do princípio da proliferação, quer de alternativas fortes, introduziria. O terceiro capítulo enfatiza, para lá dos consensos partilhados e das diferenças assumidas, a importância das contribuições de Feyerabend, Kuhn e Lakatos para a problematização das teses do neopositivismo, do racionalismo crítico e do falsificacionismo na história e filosofia da ciência.