Consulta: creatorFacets:"Pereira,Tiago Campos"
Registros recuperados: 5
Data/hora: 10/06/2024 14:04:16

Strand Analysis, a free online program for the computational identification of the best RNA interference (RNAi) targets based on Gibbs free energy
Provedor de dados: Genetics and Molecular Biology
Autores: Pereira,Tiago Campos; Bittencourt,Vinícius D'Ávila Pascoal; Secolin,Rodrigo; Rocha,Cristiane de Souza; Maia,Ivan de Godoy; Lopes-Cendes,Iscia.
The RNA interference (RNAi) technique is a recent technology that uses double-stranded RNA molecules to promote potent and specific gene silencing. The application of this technique to molecular biology has increased considerably, from gene function identification to disease treatment. However, not all small interfering RNAs (siRNAs) are equally efficient, making target selection an essential procedure. Here we present Strand Analysis (SA), a free online software tool able to identify and classify the best RNAi targets based on Gibbs free energy (deltaG). Furthermore, particular features of the software, such as the free energy landscape and deltaG gradient, may be used to shed light on RNA-induced silencing complex (RISC) activity and RNAi mechanisms,...
Tipo: Info:eu-repo/semantics/article
Palavras-chave: RNAi; SiRNA; SiRNA design; Software.
Ano: 2007
URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572007000600030

SSD - a free software for designing multimeric mono-, bi- and trivalent shRNAs
Provedor de dados: Genetics and Molecular Biology
Autores: Carli,Gabriel José de; Rotela,Abdon Troche; Lubini,Greice; Contiliani,Danyel Fernandes; Candia,Nidia Benítez; Depintor,Thiago S.; Abreu,Fabiano Carlos Pinto de; Simões,Zilá Luz Paulino; Ríos,Danilo Fernández; Pereira,Tiago Campos.
Abstract RNA interference (RNAi) is a powerful gene silencing technology, widely used in analyses of reverse genetics, development of therapeutic strategies and generation of biotechnological products. Here we present a free software tool for the rational design of RNAi effectors, named siRNA and shRNA designer (SSD). SSD incorporates our previously developed software Strand Analysis to construct template DNAs amenable for the large scale production of mono-, bi- and trivalent multimeric shRNAs, via in vitro rolling circle transcription. We tested SSD by creating a trivalent multimeric shRNA against the vitellogenin gene of Apis mellifera. RT-qPCR analysis revealed that our molecule promoted a decrease in more than 50% of the target mRNA, in a...
Tipo: Info:eu-repo/semantics/article
Palavras-chave: Gene silencing; SiRNA; Multimeric; ShRNA; Free software.
Ano: 2020
URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572020000100802

The new world of RNAs
Provedor de dados: Genetics and Molecular Biology
Autores: Dogini,Danyella Barbosa; Pascoal,Vinícius D'Avila Bittencourt; Avansini,Simoni Helena; Vieira,André Schwambach; Pereira,Tiago Campos; Lopes-Cendes,Iscia.
One of the major developments that resulted from the human genome sequencing projects was a better understanding of the role of non-coding RNAs (ncRNAs). NcRNAs are divided into several different categories according to size and function; however, one shared feature is that they are not translated into proteins. In this review, we will discuss relevant aspects of ncRNAs, focusing on two main types: i) microRNAs, which negatively regulate gene expression either by translational repression or target mRNA degradation, and ii) small interfering RNAs (siRNAs), which are involved in the biological process of RNA interference (RNAi). Our knowledge regarding these two types of ncRNAs has increased dramatically over the past decade, and they have a great potential...
Tipo: Info:eu-repo/semantics/article
Palavras-chave: Non-coding RNAs; MicroRNAs; RNA interferance; RNA-based drugs.
Ano: 2014
URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572014000200014

Analysis of energetically biased transcripts of viruses and transposable elements
Provedor de dados: Genetics and Molecular Biology
Autores: Secolin,Rodrigo; Pascoal,Vinícius D'Ávila Bitencourt; Lopes-Cendes,Iscia; Pereira,Tiago Campos.
RNA interference (RNAi) is a natural endogenous process by which double-stranded RNA molecules trigger potent and specific gene silencing in eukaryotic cells and is characterized by target RNA cleavage. In mammals, small interfering RNAs (siRNAs) are the trigger molecules of choice and constitute a new class of RNA-based antiviral agents. In an efficient RNAi response, the antisense strand of siRNAs must enter the RNA-induced silencing complex (RISC) in a process mediated by thermodynamic features. In this report, we hypothesize that silent mutations capable of inverting thermodynamic properties can promote resistance to siRNAs. Extensive computational analyses were used to assess whether continuous selective pressure that promotes such mutations could...
Tipo: Info:eu-repo/semantics/article
Palavras-chave: RNAi; SiRNA; Synonymous mutation; Viral evolution.
Ano: 2012
URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572012000500022

Multiple genes contribute to anhydrobiosis (tolerance to extreme desiccation) in the nematode Panagrolaimus superbus
Provedor de dados: Genetics and Molecular Biology
Autores: Evangelista,Cláudia Carolina Silva; Guidelli,Giovanna Vieira; Borges,Gustavo; Araujo,Thais Fenz; Souza,Tiago Alves Jorge de; Neves,Ubiraci Pereira da Costa; Tunnacliffe,Alan; Pereira,Tiago Campos.
Abstract The molecular basis of anhydrobiosis, the state of suspended animation entered by some species during extreme desiccation, is still poorly understood despite a number of transcriptome and proteome studies. We therefore conducted functional screening by RNA interference (RNAi) for genes involved in anhydrobiosis in the holo-anhydrobiotic nematode Panagrolaimus superbus. A new method of survival analysis, based on staining, and proof-of-principle RNAi experiments confirmed a role for genes involved in oxidative stress tolerance, while a novel medium-scale RNAi workflow identified a further 40 anhydrobiosis-associated genes, including several involved in proteostasis, DNA repair and signal transduction pathways. This suggests that multiple genes...
Tipo: Info:eu-repo/semantics/article
Palavras-chave: Peroxiredoxin; Kinase; RNAi; Proteostasis.
Ano: 2017
URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572017000500790