Reframing gene essentiality in terms of adaptive flexibility

Abstract Background Essentiality assays are important tools commonly utilized for the discovery of gene functions. Growth/no growth screens of single gene knockout strain collections are also often utilized to test the predictive power of genome-scale models. False positive predictions occur when computational analysis predicts a gene to be non-essential, however experimental screens deem the gene to be essential. One explanation for this inconsistency is that the model contains the wrong information, possibly an incorrectly annotated alternative pathway or isozyme reaction. Inconsistencies could also be attributed to experimental limitations, such as growth tests with arbitrary time cut-offs. The focus of this study was to resolve such inconsistencies to better understand isozyme activities and gene essentiality. Results In this study, we explored the definition of conditional essentiality from a phenotypic and genomic perspective. Gene-deletion strains associated with false positive predictions of gene essentiality on defined minimal medium for Escherichia coli were targeted for extended growth tests followed by population sequencing and transcriptome analysis. Of the twenty false positive strains available and confirmed from the Keio single gene knock-out collection, 11 strains were shown to grow with longer incubation periods making these actual true positives. These strains grew reproducibly with a diverse range of growth phenotypes. The lag phase observed for these strains ranged from less than one day to more than 7 days. It was found that 9 out of 11 of the false positive strains that grew acquired mutations in at least one replicate experiment and the types of mutations ranged from SNPs and small indels associated with regulatory or metabolic elements to large regions of genome duplication. Comparison of the detected adaptive mutations, modeling predictions of alternate pathways and isozymes, and transcriptome analysis of KO strains suggested agreement for the observed growth phenotype for 6 out of the 9 cases where mutations were observed. Conclusions Longer-term growth experiments followed by whole genome sequencing and transcriptome analysis can provide a better understanding of conditional gene essentiality and mechanisms of adaptation to such perturbations. Compensatory mutations are largely reproducible mechanisms and are in agreement with genome-scale modeling predictions to loss of function gene deletion events

Licenciamento ambiental de postos de combustíveis no município de Niterói

Os postos de combustíveis podem ser considerados de alto potencial poluidor. A partir da corrosão dos tanques de armazenamento de combustíveis, hidrocarbonetos são lançados no solo podendo causar a contaminação do lençol freático assim como explosões em áreas urbanas. O presente trabalho faz um estudo das instruções orientadoras à atividade de armazenamento e distribuição de combustível que regem a atividade de licenciamento ambiental. Além disso, é feito um estudo dos impactos ambientais da contaminação de um posto de combustível. O trabalho é voltado ao município de Niterói e dessa forma, foi realizado um levantamento das áreas contaminadas a partir da atuação de postos de combustíveis, objetivando realizar o estudo da gestão ambiental no município e o impacto local deste tipo de empreendimento. Este levantamento será determinante para o planejamento de futuras atividades nessas áreas, visto que algumas serão inviabilizadas devido ao histórico de contaminações existentes. O banco de dados aqui elaborado, será utilizado no cotidiano dos setores de licenciamento ambiental e fiscalização da SMARHS como mais uma ferramenta disponível para o gerenciamento ambiental da cidade, tendo sido uma relevante contribuição do estudoFuel stations can be considered as high potential polluters. From the corrosion of fuel storage tanks, hydrocarbons are released into the soil and can cause groundwater contamination as well as explosions in urban areas. The present work makes a study of the instructions that guide the activity of storage and distribution of fuel that govern the activity of environmental licensing. In addition, a study of the environmental impacts of contamination of a fuel station is carried out. The work is directed to the municipality of Niterói and, in this way, a survey of the contaminated areas was carried out from the fuel stations, aiming to carry out the study of the environmental management in the city and the local impact of this type of enterprise. This survey will be decisive for the planning of future activities in these areas, since some will be unfeasible due to the history of existing contaminations. The database developed here will be used in the daily activities of environmental licensing and inspections carried out by SMARHS as another available tool for environmental management of the city, and was a relevant contribution of the stud