Transcript tinkering: RNA modifications in protozoan parasites.

Apicomplexan and trypanosomatid parasites have evolved a wide range of post-transcriptional processes that allow them to replicate, differentiate, and transmit within and among multiple different tissue, host, and vector environments. In this review, we highlight the recent advances that point toward the regulatory potential of RNA modifications in mediating these processes on the coding and noncoding transcriptome throughout the life cycle of protozoan parasites. We discuss the recent technical advancements enabling the study of the 'epitranscriptome' and how parasites evolved RNA modification-mediated mechanisms adapted to their unique lifestyles.

Optimization of highly inclined illumination for diffraction-limited and super-resolution microscopy.

In HILO microscopy, a highly inclined and laminated light sheet is used to illuminate the sample, thus drastically reducing background fluorescence in wide-field microscopy, but maintaining the simplicity of the use of a single objective for both illumination and detection. Although the technique has become widely popular, particularly in single molecule and super-resolution microscopy, a limited understanding of how to finely shape the illumination beam and of how this impacts on the image quality complicates the setting of HILO to fit the experimental needs. In this work, we build up a simple and comprehensive guide to optimize the beam shape and alignment in HILO and to predict its performance in conventional fluorescence and super-resolution microscopy.

Characterization of substituted piperazines able to reverse MDR in Escherichia coli strains overexpressing resistance-nodulation-cell division (RND) efflux pumps.

Background: MDR in bacteria is threatening to public health. Overexpression of efflux pumps is an important cause of MDR. The co-administration of antimicrobial drugs and efflux pump inhibitors (EPIs) is a promising approach to address the problem of MDR.

1-benzyl-1,4-diazepane reduces the efflux of resistance-nodulation-cell division pumps in .

To investigate the action mechanism of 1-benzyl-1,4-diazepane (1-BD) as efflux pump inhibitor (EPI) in mutants: Δ or overexpressing AcrAB and AcrEF efflux pumps. Effect of 1-BD on: antibiotic potentiation, by microdilution method; membrane functionality, by fluorimetric assays; ethidium bromide accumulation, by fluorometric real-time efflux assay; AcrB expression, by quantitative photoactivated localization microscopy. 1-BD decreases the minimal inhibitory concentration of levofloxacin and other antibiotics and increase ethidium bromide accumulation in overexpressing efflux pumps but not in the Δ strain.

Creation and Characterization of a Genomically Hybrid Strain in the Nitrogen-Fixing Symbiotic Bacterium Sinorhizobium meliloti.

Many bacteria, often associated with eukaryotic hosts and of relevance for biotechnological applications, harbor a multipartite genome composed of more than one replicon. Biotechnologically relevant phenotypes are often encoded by genes residing on the secondary replicons. A synthetic biology approach to developing enhanced strains for biotechnological purposes could therefore involve merging pieces or entire replicons from multiple strains into a single genome.

Template-Assisted Metabolic Reconstruction and Assembly of Hybrid Bacterial Models.

Intraspecific genomic exchanges happen frequently between bacteria living in the same natural environment and can also be performed artificially in the laboratory for basic research or genetic/metabolic engineering purposes. In silico metabolic reconstruction and simulation of the metabolism of the hybrid strains that result from these processes can be used to predict the phenotypic outcome of such genomic rearrangements; this can be especially helpful as a designing tool in the purview of synthetic biology. However, reconstructing the metabolism of a bacterium with a hybrid genome through in silico approaches is not a trivial task, as it requires taking into account the complex relationships existing between metabolic genes and how they change (or remain unchanged) when new genes are placed in a different genomic context.

Investigation on torquetenovirus (TTV) microRNA transcriptome in vivo.

Torquetenovirus (TTV) is a widespread anellovirus that establishes persistent infections in human showing an increased viremia in immunosuppressed patients. TTV possesses microRNA (miRNA)-coding sequences that might be involved in viral immune evasion. Here, the presence of TTV DNA and miRNAs expression was investigated in plasma samples of 77 diseased (20 infected with human immunodeficiency virus (HIV), 18 infected with hepatitis B (HBV) virus, 18 infected with hepatitis C (HCV) virus, 21 solid organ transplanted) patients, and 25 healthy controls.