Triplet Repeat–Derived siRNAs Enhance RNA–Mediated Toxicity in a Drosophila Model for Myotonic Dystrophy

More than 20 human neurological and neurodegenerative diseases are caused by simple DNA repeat expansions; among these, non-coding CTG repeat expansions are the basis of myotonic dystrophy (DM1). Recent work, however, has also revealed that many human genes have anti-sense transcripts, raising the possibility that human trinucleotide expansion diseases may be comprised of pathogenic activities due both to a sense expanded-repeat transcript and to an anti-sense expanded-repeat transcript. We established a Drosophila model for DM1 and tested the role of interactions between expanded CTG transcripts and expanded CAG repeat transcripts. These studies revealed dramatically enhanced toxicity in flies co-expressing CTG with CAG expanded repeats. Expression of the two transcripts led to novel pathogenesis with the generation of dcr-2 and ago2-dependent 21-nt triplet repeat-derived siRNAs. These small RNAs targeted the expression of CAG-containing genes, such as Ataxin-2 and TATA binding protein (TBP), which bear long CAG repeats in both fly and man. These findings indicate that the generation of triplet repeat-derived siRNAs may dramatically enhance toxicity in human repeat expansion diseases in which anti-sense transcription occurs

Transcriptional control in the prereplicative phase of T4 development

Control of transcription is crucial for correct gene expression and orderly development. For many years, bacteriophage T4 has provided a simple model system to investigate mechanisms that regulate this process. Development of T4 requires the transcription of early, middle and late RNAs. Because T4 does not encode its own RNA polymerase, it must redirect the polymerase of its host, E. coli, to the correct class of genes at the correct time. T4 accomplishes this through the action of phage-encoded factors. Here I review recent studies investigating the transcription of T4 prereplicative genes, which are expressed as early and middle transcripts. Early RNAs are generated immediately after infection from T4 promoters that contain excellent recognition sequences for host polymerase. Consequently, the early promoters compete extremely well with host promoters for the available polymerase. T4 early promoter activity is further enhanced by the action of the T4 Alt protein, a component of the phage head that is injected into E. coli along with the phage DNA. Alt modifies Arg265 on one of the two α subunits of RNA polymerase. Although work with host promoters predicts that this modification should decrease promoter activity, transcription from some T4 early promoters increases when RNA polymerase is modified by Alt. Transcription of T4 middle genes begins about 1 minute after infection and proceeds by two pathways: 1) extension of early transcripts into downstream middle genes and 2) activation of T4 middle promoters through a process called sigma appropriation. In this activation, the T4 co-activator AsiA binds to Region 4 of σ70, the specificity subunit of RNA polymerase. This binding dramatically remodels this portion of σ70, which then allows the T4 activator MotA to also interact with σ70. In addition, AsiA restructuring of σ70 prevents Region 4 from forming its normal contacts with the -35 region of promoter DNA, which in turn allows MotA to interact with its DNA binding site, a MotA box, centered at the -30 region of middle promoter DNA. T4 sigma appropriation reveals how a specific domain within RNA polymerase can be remolded and then exploited to alter promoter specificity

Analysis of renal diffusion-weighted imaging (DWI) using apparent diffusion coefficient (ADC) and intravoxel incoherent motion (IVIM) models

Analysis of renal diffusion-weighted imaging (DWI) data to derive markers of tissue properties requires careful consideration of the type, extent, and limitations of the acquired data. Alongside data quality and general suitability for quantitative analysis, choice of diffusion model, fitting algorithm, and processing steps can have consequences for the precision, accuracy, and reliability of derived diffusion parameters. Here we introduce and discuss important steps for diffusion-weighted image processing, and in particular give example analysis protocols and pseudo-code for analysis using the apparent diffusion coefficient (ADC) and intravoxel incoherent motion (IVIM) models. Following an overview of general principles, we provide details of optional steps, and steps for validation of results. Illustrative examples are provided, together with extensive notes discussing wider context of individual steps, and notes on potential pitfalls.This publication is based upon work from the COST Action PARENCHIMA, a community-driven network funded by the European Cooperation in Science and Technology (COST) program of the European Union, which aims to improve the reproducibility and standardization of renal MRI biomarkers. This analysis protocol chapter is complemented by two separate chapters describing the basic concepts and experimental procedure

Análise do emprego do cálculo amostral e do erro do método em pesquisas científicas publicadas na literatura ortodôntica nacional e internacional Analysis of the use of sample size calculation and error of method in researches published in Brazilian and international orthodontic journals

INTRODUÇÃO: o dimensionamento adequado da amostra estudada e a análise apropriada do erro do método são passos importantes na validação dos dados obtidos em determinado estudo científico, além das questões éticas e econômicas. OBJETIVO: esta investigação tem o objetivo de avaliar, quantitativamente, com que frequência os pesquisadores da ciência ortodôntica têm empregado o cálculo amostral e a análise do erro do método em pesquisas publicadas no Brasil e nos Estados Unidos. MÉTODOS: dois importantes periódicos, de acordo com a Capes (Coordenação de Aperfeiçoamento de Pessoal de Nível Superior), foram analisados, a Revista Dental Press de Ortodontia e Ortopedia Facial (Dental Press) e o American Journal of Orthodontics and Dentofacial Orthopedics (AJO-DO). Apenas artigos publicados entre os anos de 2005 e 2008 foram analisados. RESULTADOS: a maioria das pesquisas publicadas em ambas as revistas emprega alguma forma de análise do erro do método, quando essa metodologia pode ser aplicada. Porém, apenas um número muito pequeno dos artigos publicados nesses periódicos apresenta qualquer descrição de como foram dimensionadas as amostras estudadas. Essa proporção, já pequena (21,1%) na revista editada nos Estados Unidos (AJO-DO), é significativamente menor (p=0,008) na revista editada no Brasil (Dental Press) (3,9%). CONCLUSÃO: os pesquisadores e o corpo editorial, de ambas as revistas, deveriam dedicar uma maior atenção ao exame dos erros inerentes à ausência de tais análises na pesquisa científica, em especial aos erros inerentes a um dimensionamento inadequado das amostras.<br>INTRODUCTION: Reliable sample size and an appropriate analysis of error are important steps to validate the data obtained in a scientific study, in addition to the ethical and economic issues. OBJECTIVE: To evaluate, quantitatively, how often the researchers of orthodontic science have used the calculation of sample size and evaluated the method error in studies published in Brazil and in the United States of America. METHODS: Two major journals, according to CAPES (Brazilian Federal Agency for Support and Evaluation of Graduate Education), were analyzed through a hand search: Revista Dental Press de Ortodontia e Ortopedia Facial and the American Journal of Orthodontics and Dentofacial Orthopedics (AJO-DO). Only papers published between 2005 and 2008 were examined. RESULTS: Most of surveys published in both journals employed some method of error analysis, when this methodology can be applied. On the other hand, only a very small number of articles published in these journals have any description of how sample size was calculated. This proportion was 21.1% for the journal published in the United States (AJO-DO), and was significantly lower (p= 0.008) for the journal of orthodontics published in Brazil (3.9%). CONCLUSION: Researchers and the editorial board of both journals should drive greater concern for the examination of errors inherent in the absence of such analyses in scientific research, particularly the errors related to the use of an inadequate sample size