Temporal progress of gene expression analysis with RNA-Seq data: A review on the relationship between computational methods.

Analysis of differential gene expression from RNA-seq data has become a standard for several research areas. The steps for the computational analysis include many data types and file formats, and a wide variety of computational tools that can be applied alone or together as pipelines. This paper presents a review of the differential expression analysis pipeline, addressing its steps and the respective objectives, the principal methods available in each step, and their properties, therefore introducing an organized overview to this context. This review aims to address mainly the aspects involved in the differentially expressed gene (DEG) analysis from RNA sequencing data (RNA-seq), considering the computational methods. In addition, a timeline of the computational methods for DEG is shown and discussed, and the relationships existing between the most important computational tools are presented by an interaction network. A discussion on the challenges and gaps in DEG analysis is also highlighted in this review. This paper will serve as a tutorial for new entrants into the field and help established users update their analysis pipelines.

RNA-Seq differential expression analysis: An extended review and a software tool.

The correct identification of differentially expressed genes (DEGs) between specific conditions is a key in the understanding phenotypic variation. High-throughput transcriptome sequencing (RNA-Seq) has become the main option for these studies. Thus, the number of methods and softwares for differential expression analysis from RNA-Seq data also increased rapidly. However, there is no consensus about the most appropriate pipeline or protocol for identifying differentially expressed genes from RNA-Seq data. This work presents an extended review on the topic that includes the evaluation of six methods of mapping reads, including pseudo-alignment and quasi-mapping and nine methods of differential expression analysis from RNA-Seq data. The adopted methods were evaluated based on real RNA-Seq data, using qRT-PCR data as reference (gold-standard). As part of the results, we developed a software that performs all the analysis presented in this work, which is freely available at https://github.com/costasilvati/consexpression. The results indicated that mapping methods have minimal impact on the final DEGs analysis, considering that adopted data have an annotated reference genome. Regarding the adopted experimental model, the DEGs identification methods that have more consistent results were the limma+voom, NOIseq and DESeq2. Additionally, the consensus among five DEGs identification methods guarantees a list of DEGs with great accuracy, indicating that the combination of different methods can produce more suitable results. The consensus option is also included for use in the available software.

Demarcação abdominal por enfermeira estomoterapêuta / Marcación abdominal del estoma en pacientes oncológicos por enfermera estomoterapeuta / Abdominal demarcation stoma in oncological patients by stomotherapy nurse

Resumo 20. Trata-se de uma revisão integrativa, cujo foco de estudo é a atuação do enfermeiro estomaterapeuta na demarcação do estoma intestinal em clientes submetidos à cirurgia oncológica. Objetivos: realizar levantamento da produção de artigos científicos referentes ao tema proposto; discutir as ações específicas utilizadas pelo enfermeiro estomaterapeuta na demarcação dos estomas intestenais em pacientes oncológicos. Foi realizado um levantamento de produções científicas nas seguintes bases eletrônicas: LILACS, SCIELO, periódicos CAPES. Durante a pesquisa, foram encontrados 292 artigos referentes aos anos de 1998 a 2013, porém, somente 4 artigos respondem ao critério de inclusão. Através destes documentos, foi realizada leitura analítica organizada em 3 temas: caracterização dos artigos; demarcação do estoma e peculiaridades da demarcação no paciente oncológico. Esta pesquisa demonstrou que, nas bases de dados incluídas, não há publicações recentes que incluam as peculiaridades dos pacientes oncológicos no tocante a demarcação do estoma, sendo necessária a utilização de literatura de oncologia para enriquecer a discussão. Conclui-se que o reconhecimento da demarcação realizada pelo enfermeiro estomaterapeuta ainda se faz pouco conhecida no âmbito da saúde, sendo assim necessário intensificar os estudos nesta área para esta especialização seja cada vez mais reconhecida, visando assim um cuidado específico e individual, colaborando com a qualidade dos cuidados de saúde das pessoas.

Resumen 25. Es una revisión integradora, cuyo objeto de estudio es el papel de la enfermera estomaterapeuta en la marcación del estoma intestinal en clientes de cirugía oncológica. Los objetivos son realizar un estudio de la producción de artículos científicos sobre el tema propuesto y discutir acciones específicas utilizadas por la enfermera estomaterapeuta en la demarcación de los estomas intestinales en pacientes con cáncer. Realizamos un estudio de las producciones científicas en las siguientes bases electrónicas: LILACS, SCIELO y Revistas CAPES. Durante la búsqueda se encontraron 292 artículos, publicados durante los años de 1998 a 2013; sin embargo, sólo 4 artículos responden a los criterios de inclusión. A través de estos documentos fue realizada una lectura analítica organizada en tres temas: caracterización de los artículos; marcación del estoma y las peculiaridades de la marcación en el paciente oncológico. Esta investigación ha demostrado que, en las bases de datos incluidas, no hay publicaciones recientes que incluyan las peculiaridades de los pacientes de cáncer con respecto a la marcación del estoma, siendo necesaria la utilización de la literatura de oncología para enriquecer la discusión. Se concluye que el reconocimiento de la marcación que hace la enfermera estomaterapeuta es todavía poco conocido en el campo de la salud, por lo que es necesario intensificar los estudios en esta área para que esta especialización sea cada vez más reconocida, con el objetivo de una atención específica e individual, colaborando con la calidad de la atención de salud de las personas.

Abstract 28. It is an integrative review, focused in the role of the ostomy nurse in the demarcation of intestinal stoma in oncologic surgery clients. Objectives: to conduct a survey of production of scientific articles concerning the proposed topic and to discuss specific actions carried out by the ostomy nurse on the demarcation of the stomata intestinal in such patients. We conducted a survey of scientific productions in the following electronic bases: LILACS, SCIELO and CAPES journals. During the search, 292 articles were found for the years 1998 to 2013; however, only 4 articles meet the inclusion criteria. Through these documents an analytical reading was organized in three topics: characterization of the articles, demarcation of the stoma, and peculiarities of the demarcation in the oncologic patient. This research has shown that in these databases there are no recent publications that include the peculiarities of cancer patients regarding demarcation of the stoma, requiring the use of oncology literature to enrich the discussion. It is concluded that the recognition of the marking done by the ostomy nurse is still little known in the field of health, making it necessary to intensify studies in this area for this performance to be increasingly recognized, aiming at a specific and individualized care, collaborating with the quality of health care of people.

Genome-wide analysis of EgEVE_1, a transcriptionally active endogenous viral element associated to small RNAs in Eucalyptus genomes.

Endogenous viral elements (EVEs) are the result of heritable horizontal gene transfer from viruses to hosts. In the last years, several EVE integration events were reported in plants by the exponential availability of sequenced genomes. Eucalyptus grandis is a forest tree species with a sequenced genome that is poorly studied in terms of evolution and mobile genetic elements composition. Here we report the characterization of E. grandis endogenous viral element 1 (EgEVE_1), a transcriptionally active EVE with a size of 5,664 bp. Phylogenetic analysis and genomic distribution demonstrated that EgEVE_1 is a newly described member of the Caulimoviridae family, distinct from the recently characterized plant Florendoviruses. Genomic distribution of EgEVE_1 and Florendovirus is also distinct. EgEVE_1 qPCR quantification in Eucalyptus urophylla suggests that this genome has more EgEVE_1 copies than E. grandis. EgEVE_1 transcriptional activity was demonstrated by RT-qPCR in five Eucalyptus species and one intrageneric hybrid. We also identified that Eucalyptus EVEs can generate small RNAs (sRNAs),that might be involved in de novo DNA methylation and virus resistance. Our data suggest that EVE families in Eucalyptus have distinct properties, and we provide the first comparative analysis of EVEs in Eucalyptus genomes.

Genome-wide analysis of EgEVE_1, a transcriptionally active endogenous viral element associated to small RNAs in Eucalyptus genomes

Abstract Endogenous viral elements (EVEs) are the result of heritable horizontal gene transfer from viruses to hosts. In the last years, several EVE integration events were reported in plants by the exponential availability of sequenced genomes. Eucalyptus grandis is a forest tree species with a sequenced genome that is poorly studied in terms of evolution and mobile genetic elements composition. Here we report the characterization of E. grandis endogenous viral element 1 (EgEVE_1), a transcriptionally active EVE with a size of 5,664 bp. Phylogenetic analysis and genomic distribution demonstrated that EgEVE_1 is a newly described member of the Caulimoviridae family, distinct from the recently characterized plant Florendoviruses. Genomic distribution of EgEVE_1 and Florendovirus is also distinct. EgEVE_1 qPCR quantification in Eucalyptus urophylla suggests that this genome has more EgEVE_1 copies than E. grandis. EgEVE_1 transcriptional activity was demonstrated by RT-qPCR in five Eucalyptus species and one intrageneric hybrid. We also identified that Eucalyptus EVEs can generate small RNAs (sRNAs),that might be involved in de novo DNA methylation and virus resistance. Our data suggest that EVE families in Eucalyptus have distinct properties, and we provide the first comparative analysis of EVEs in Eucalyptus genomes.

Intravenous and intra-arterial administration of bone marrow mononuclear cells after focal cerebral ischemia: Is there a difference in biodistribution and efficacy?

Intravascular delivery of cells has been increasingly used in stroke models and clinical trials. We compared the biodistribution and therapeutic effects of bone marrow mononuclear cells (BMMCs) delivered by intra-arterial (IA) or intravenous (IV) injection after cortical ischemia. For the biodistribution analyses, BMMCs were labeled with (99m)Technetium ((99m)Tc). At 2 h, gamma-well counting of the brain and of the other organs evaluated did not show differences between the non-ischemic and ischemic groups or between injection routes, and the organs with the highest uptake were the liver and lungs, with low uptake in the brain. At 24 h, the liver maintained the highest activity, and a marked decrease was seen in pulmonary uptake in all groups. At this time point, although the activity in the brain remained low, the lesioned hemisphere showed greater homing than the contralateral hemisphere, for both the IV and IA ischemic groups. Histological analysis by CellTrace labeling indicated similar homing between both routes in the peri-infarct region 24 h after transplantation and functional recovery was observed in both groups up to 11 weeks after the lesion. In conclusion, transplantation of BMMCs by IA or IV routes may lead to similar brain homing and therapeutic efficacy after experimental stroke.