Functional Analyses of the Three Simian Hemorrhagic Fever Virus Nonstructural Protein 1 Papain-Like Proteases

The N-terminal region of simian hemorrhagic fever virus (SHFV) nonstructural polyprotein 1a is predicted to encode three papain-like proteases (PLP1α, PLP1β, and PLP1γ). Catalytic residues and cleavage sites for each of the SHFV PLP1s were predicted by alignment of the SHFV PLP1 region sequences with each other as well as with those of other arteriviruses, and the predicted catalytic residues were shown to be proximal by homology modeling of the SHFV nsp1s on porcine respiratory and reproductive syndrome virus (PRRSV) nsp1 crystal structures. The functionality of the predicted catalytic Cys residues and cleavage sites was tested by analysis of the autoproteolytic products generated in in vitro transcription/translation reactions done with wild-type or mutant SHFV nsp1 constructs. Cleavage sites were also analyzed by mass spectroscopy analysis of selected immunoprecipitated cleavage products. The data showed that each of the three SHFV PLP1s is an active protease. Cys63 was identified as the catalytic Cys of SHFV PLP1α and is adjacent to an Ala instead of the canonical Tyr observed in other arterivirus PLP1s. SHFV PLP1γ is able to cleave at both downstream and upstream nsp1 junction sites. Although intermediate precursor polyproteins as well as alternative products generated by each of the SHFV PLP1s cleaving at sites within the N-terminal region of nsp1β were produced in the in vitro reactions, Western blotting of SHFV-infected, MA104 cell lysates with SHFV nsp1 protein-specific antibodies detected only the three mature nsp1 proteins

Governing Uncertainty in a Secular Age: Rationalities of Violence, Theodicy and Torture

This article explores the problem of governing uncertainty in a secular age by focusing on the theological notion of ‘theodicy’ as the underlying rationale for the use of torture in the so-called ‘war on terror’. With God’s departure from the world, the problem of uncertainty acquires new salience as human beings can no longer explain tragic events as part of a transcendent order and must find immanent causes for the ‘evils’ that surround them. Taking a cue from Max Weber, I discuss how the problem of theodicy – how to reconcile the existence of God with the presence of evil in the world – does not disappear in the secular age but is mobilized through a Foucauldian biopolitical logic. Secular theodicy governs uncertainty through the production of economies of knowledge that rationalize processes of criminalization and securitization of entire groups and justify the use of violence. This process is particularly striking when analysing the use of torture in the so-called ‘war on terror’. Through a comparison with medieval practices and focusing on the cases of Guantanamo and Abu Ghraib, the article shows how secular torture is the product of a biopolitical theodicy aimed at governing uncertainty through the construction of the tortured as immanent evils who threaten our ‘good life’ and ‘deserve’ their treatment. Secular theodicy turns torture into an extreme form of governmentality of uncertainty in which the disciplining of conduct becomes the construction of subjectivities based on essentialist, stereotypical and racist – and for these very reasons, reassuring – economies of knowledge

DNA methylation, transcriptome and genetic copy number signatures of diffuse cerebral WHO grade II/III gliomas resolve cancer heterogeneity and development

Background: Diffuse lower WHO grade II and III gliomas (LGG) are slowly progressing brain tumors, many of which eventually transform into a more aggressive type. LGG is characterized by widespread genetic and transcriptional heterogeneity, yet little is known about the heterogeneity of the DNA methylome, its function in tumor biology, coupling with the transcriptome and tumor microenvironment and its possible impact for tumor development. Methods: We here present novel DNA methylation data of an LGG-cohort collected in the German Glioma Network containing about 85% isocitrate dehydrogenase (IDH) mutated tumors and performed a combined bioinformatics analysis using patient-matched genome and transcriptome data. Results: Stratification of LGG based on gene expression and DNA-methylation provided four consensus subtypes. We characterized them in terms of genetic alterations, functional context, cellular composition, tumor microenvironment and their possible impact for treatment resistance and prognosis. Glioma with astrocytoma-resembling phenotypes constitute the largest fraction of nearly 60%. They revealed largest diversity and were divided into four expression and three methylation groups which only partly match each other thus reflecting largely decoupled expression and methylation patterns. We identified a novel G-protein coupled receptor and a cancer-related ‘keratinization’ methylation signature in in addition to the glioma-CpG island methylator phenotype (G-CIMP) signature. These different signatures overlap and combine in various ways giving rise to diverse methylation and expression patterns that shape the glioma phenotypes. The decrease of global methylation in astrocytoma-like LGG associates with higher WHO grade, age at diagnosis and inferior prognosis. We found analogies between astrocytoma-like LGG with grade IV IDH-wild type tumors regarding possible worsening of treatment resistance along a proneural-to-mesenchymal axis. Using gene signature-based inference we elucidated the impact of cellular composition of the tumors including immune cell bystanders such as macrophages. Conclusions: Genomic, epigenomic and transcriptomic factors act in concert but partly also in a decoupled fashion what underpins the need for integrative, multidimensional stratification of LGG by combining these data on gene and cellular levels to delineate mechanisms of gene (de-)regulation and to enable better patient stratification and individualization of treatment

Patterns, predictors and prognostic relevance of high-grade hematotoxicity after temozolomide or temozolomide-lomustine in the CeTeG/NOA-09 trial

PURPOSE: In the randomized phase III trial CeTeG/NOA-09, temozolomide (TMZ)/lomustine (CCNU) combination therapy was superior to TMZ in newly diagnosed MGMT methylated glioblastoma, albeit reporting more frequent hematotoxicity. Here, we analyze high grade hematotoxicity and its prognostic relevance in the trial population. METHODS: Descriptive and comparative analysis of hematotoxicity adverse events ≥ grade 3 (HAE) according to the Common Terminology of Clinical Adverse Events, version 4.0 was performed. The association of HAE with survival was assessed in a landmark analysis. Logistic regression analysis was performed to predict HAE during the concomitant phase of chemotherapy. RESULTS: HAE occurred in 36.4% and 28.6% of patients under CCNU/TMZ and TMZ treatment, respectively. The median onset of the first HAE was during concomitant chemotherapy (i.e. first CCNU/TMZ course or daily TMZ therapy), and 42.9% of patients with HAE receiving further courses experienced repeat HAE. Median HAE duration was similar between treatment arms (CCNU/TMZ 11.5; TMZ 13 days). Chemotherapy was more often discontinued due to HAE in CCNU/TMZ than in TMZ (19.7 vs. 6.3%, p = 0.036). The occurrence of HAE was not associated with survival differences (p = 0.76). Regression analysis confirmed older age (OR 1.08) and female sex (OR 2.47), but not treatment arm, as predictors of HAE. CONCLUSION: Older age and female sex are associated with higher incidence of HAE. Although occurrence of HAE was not associated with shorter survival, reliable prediction of patients at risk might be beneficial to allow optimal management of therapy and allocation of supportive measures. TRIAL REGISTRATION: NCT01149109

Processos de democracia direta: sim ou não? Os argumentos clássicos à luz da teoria e da prática

Regularmente surgem controvérsias sobre os processos de democracia direta, dos quais os mecanismos mais frequentes são a iniciativa popular, o plebiscito e o referendo. Por um lado, há autores que defendem a posição de que essas instituições tornam o jogo político mais lento, caro, confuso e ilegítimo; outros defendem a posição contrária e argumentam que processos de democracia direta são fundamentais para os cidadãos e a qualidade da democracia. O presente estudo analisa esse tema em torno de sete questões, baseadas em considerações teóricas e pesquisas empíricas: 1. A questão entre o minimalismo e o maximalismo democrático; 2. A concorrência entre maioria e minoria; 3. A concorrência entre as instituições representativas e os processos de democracia direta; 4. A questão da competência dos cidadãos; 5. A questão dos efeitos colaterais dos processos de democracia direta; 6. A questão do tamanho do eleitorado; 7. A questão dos custos dos processos de democracia direta. As sete questões são analisadas a partir de uma revisão bibliográfica que considera tanto fontes nacionais como internacionais. O estudo mostra que os processos de democracia direta podem ser um complemento para as instituições representativas em um sistema democrático. O bom desempenho dos plebiscitos, referendos e iniciativas populares depende tanto da regulamentação destes como também do desempenho das outras instituições políticas e da situação socioeconômica de um país. O estudo permite ampliar e aprofundar o debate sobre processos de democracia direta no Brasil

GJB2 mutations, GJB6 mutations and their relevance for childhood deafness

Einleitung: Zumindest 50% aller konnatalen Schwerhörigkeiten sind genetisch bedingt. Mutationen im GJB -Gen werden am häufigsten gefunden, sie liegen bei 20 bis 30% aller Patienten mit nicht syndromalen Schwerhörigkeiten vor. Wir stellten uns die Frage, ob eine weitere Differenzierung sinnvoll ist. Methode: Bei 303 Patienten mit nicht syndromaler Schwerhörigkeit wurde eine Sequenzierung des GJB2 -Gens durchgeführt . Ergebnisse: Bei den 303 Patienten mit einer nicht syndromalen Schwerhörigkeit identifizierten wir auf 156 mutierten Allelen 27 verschiedene Mutationen des GJB2 -Gens, und zwar 10 trunkierende (T) Mutationen auf 107 Allelen und 17 nicht trunkierende (NT) Mutationen auf 49 Allelen. 61 Patienten (20,1%) zeigten homozygote GJB2-Mutationen, dabei traten 21 verschiedene Genotypen auf, die in 8 homozygot trunkierende (T/T), 8 compound heterozygote (T/NT) und 5 homozygot nicht trunkierende Mutationen weiter differenziert werden konnten. Bei den homozygot trunkierenden Mutationen war der Hörverlust ausgeprägter (p=0,000058). Bei 5 der 61 Patienten trat eine Progredienz der Hörstörung auf, davon lag bei 2 eine homozygot trunkierende Mutation vor. Schlussfolgerung: Eine Differenzierung der GJB2 -Mutationen in trunkierende und nicht trunkierende scheint sinnvoll