Pan-genomic analyses of 47 complete genomes of the Rickettsia genus and prediction of new vaccine targets and virulence factors of the species.

The genus Rickettsia belongs to the Proteobacteria phylum and these bacteria infect animals and humans causing a range of diseases worldwide. The genus is divided into 4 groups and despite the public health threat and the knowledge accumulated so far, the mandatory intracellular bacteria behaviour and limitation for in vitro culture makes it difficult to create new vaccines and drug targets to these bacteria. In an attempt to overcome these limitations, pan-genomic approaches has used 47 genomes of the genus Rickettsia, in order to describe species similarities and genomics islands. Moreover, we conducted reverse vaccinology and docking analysis aiming the identification of proteins that have great potential to become vaccine and drug targets. We found out that the bacteria of the four Rickettsia groups have a high similarity with each other, with about 90 to 100% of identity. A pathogenicity island and a resistance island were predicted. In addition, 8 proteins were also predicted as strong candidates for vaccine and 9 as candidates for drug targets. The prediction of the proteins leads us to believe in a possibility of prospecting potential drugs or creating a polyvalent vaccine, which could reach most strains of this large group of bacteria.Communicated by Ramaswamy H. Sarma.

Comparative proteomic analysis of four biotechnological strains Lactococcus lactis through label-free quantitative proteomics.

Lactococcus lactis is a bacteria with high biotechnological potential, where is frequently used in the amino acid production and production of fermented dairy products, as well as drug delivery systems and mucosal vaccine vector. The knowledge of a functional core proteome is important extremely for both fundamental understanding of cell functions and for synthetic biology applications. In this study, we characterized the L. lacits proteome from proteomic analysis of four biotechnological strains L. lactis: L. lactis subsp. lactis NCDO2118, L. lactis subsp. lactis IL1403, L. lactis subsp. cremoris NZ9000 and L. lactis subsp. cremoris MG1363. Our label-free quantitative proteomic analysis of the whole bacterial lysates from each strains resulted in the characterization of the L. lactis core proteome that was composed by 586 proteins, which might contribute to resistance of this bacterium to different stress conditions as well as involved in the probiotic characteristic of L. lactis. Kegg enrichment analysis shows that ribosome, metabolic pathways, pyruvate metabolism and microbial metabolism in diverse environments were the most enriched. According to our quantitative proteomic analysis, proteins related to translation process were the more abundant in the core proteome, which represent an important step in the synthetic biology. In addition, we identified a subset of conserved proteins that are exclusive of the L. lactis subsp. cremoris or L. lactis subsp. lactis, which some are related to metabolic pathway exclusive. Regarding specific proteome of NCDO2118, we detected 'strain-specific proteins'. Finally, proteogenomics analysis allows the identification of proteins, which were not previously annotated in IL1403 and MG1363. The results obtained in this study allowed to increase our knowledge about the biology of L. lactis, which contributes to the implementation of strategies that make it possible to increase the biotechnological potential of this bacterium.

Insight of Genus Corynebacterium: Ascertaining the Role of Pathogenic and Non-pathogenic Species.

This review gathers recent information about genomic and transcriptomic studies in the Corynebacterium genus, exploring, for example, prediction of pathogenicity islands and stress response in different pathogenic and non-pathogenic species. In addition, is described several phylogeny studies to Corynebacterium, exploring since the identification of species until biological speciation in one species belonging to the genus Corynebacterium. Important concepts associated with virulence highlighting the role of Pld protein and Tox gene. The adhesion, characteristic of virulence factor, was described using the sortase mechanism that is associated to anchorage to the cell wall. In addition, survival inside the host cell and some diseases, were too addressed for pathogenic corynebacteria, while important biochemical pathways and biotechnological applications retain the focus of this review for non-pathogenic corynebacteria. Concluding, this review broadly explores characteristics in genus Corynebacterium showing to have strong relevance inside the medical, veterinary, and biotechnology field.

Analyses of the probiotic property and stress resistance-related genes of Lactococcus lactis subsp. lactis NCDO 2118 through comparative genomics and in vitro assays.

Lactococcus lactis subsp. lactis NCDO 2118 was recently reported to alleviate colitis symptoms via its anti-inflammatory and immunomodulatory activities, which are exerted by exported proteins that are not produced by L. lactis subsp. lactis IL1403. Here, we used in vitro and in silico approaches to characterize the genomic structure, the safety aspects, and the immunomodulatory activity of this strain. Through comparative genomics, we identified genomic islands, phage regions, bile salt and acid stress resistance genes, bacteriocins, adhesion-related and antibiotic resistance genes, and genes encoding proteins that are putatively secreted, expressed in vitro and absent from IL1403. The high degree of similarity between all Lactococcus suggests that the Symbiotic Islands commonly shared by both NCDO 2118 and KF147 may be responsible for their close relationship and their adaptation to plants. The predicted bacteriocins may play an important role against the invasion of competing strains. The genes related to the acid and bile salt stresses may play important roles in gastrointestinal tract survival, whereas the adhesion proteins are important for persistence in the gut, culminating in the competitive exclusion of other bacteria. Finally, the five secreted and expressed proteins may be important targets for studies of new anti-inflammatory and immunomodulatory proteins. Altogether, the analyses performed here highlight the potential use of this strain as a target for the future development of probiotic foods.

Does fish oil or folic acid prevent vascular changes in female progeny caused by maternal exposure to fluoxetine?

AIMS: Fluoxetine (FLX) is an antidepressant worldwide prescribed throughout life stages, including pregnancy and breastfeeding. Out of pregnancy, the combination of FLX with fish oil (FO) and folic acid (FA) is carried to enhance the therapeutic activity and reduce the side effects of the antidepressant. During pregnancy, FO and FA have been used to promote fetal development, and reduce, in mother, the risk of gestational and post-pregnancy depression. To evaluate if maternal exposure during pregnancy and lactation to FLX associated with FO or FA would prevent the antidepressant side effects in aorta reactivity and nitric oxide metabolites (NOx) plasmatic levels. We also sought to understand, in female offspring, the vascular effects of intrauterine and lactation exposure to FO and FA monotherapy. MAIN METHODS: Wistar rats were treated with water (control group), FLX (5mg/kg/day), FO (1.3g/kg/day), FA (3mg/kg/day), FLX+FO and FLX+FA, throughout pregnancy and lactation. On adulthood, in female offspring were evaluated the vascular reactivity to phenylephrine (Phe), the NOx and homocysteine (HCY) plasmatic levels. KEY FINDINGS: The developmental exposure to the associations of FO or FA with FLX did not correct the aortic hyporreactivity and increased NOx levels induced by intrauterine and lactation exposure to FLX. Also, isolated exposure to FO and FA did not interfere with Phe-induced aortic contraction and neither interferes with NOx and HCY plasmatic levels. SIGNIFICANCE: The developmental exposure to FO and FA was safe for vascular function of female offspring but did not prevent the vascular effects of FLX-exposure.

SIMBA: a web tool for managing bacterial genome assembly generated by Ion PGM sequencing technology.

BACKGROUND: The evolution of Next-Generation Sequencing (NGS) has considerably reduced the cost per sequenced-base, allowing a significant rise of sequencing projects, mainly in prokaryotes. However, the range of available NGS platforms requires different strategies and software to correctly assemble genomes. Different strategies are necessary to properly complete an assembly project, in addition to the installation or modification of various software. This requires users to have significant expertise in these software and command line scripting experience on Unix platforms, besides possessing the basic expertise on methodologies and techniques for genome assembly. These difficulties often delay the complete genome assembly projects. RESULTS: In order to overcome this, we developed SIMBA (SImple Manager for Bacterial Assemblies), a freely available web tool that integrates several component tools for assembling and finishing bacterial genomes. SIMBA provides a friendly and intuitive user interface so bioinformaticians, even with low computational expertise, can work under a centralized administrative control system of assemblies managed by the assembly center head. SIMBA guides the users to execute assembly process through simple and interactive pages. SIMBA workflow was divided in three modules: (i) projects: allows a general vision of genome sequencing projects, in addition to data quality analysis and data format conversions; (ii) assemblies: allows de novo assemblies with the software Mira, Minia, Newbler and SPAdes, also assembly quality validations using QUAST software; and (iii) curation: presents methods to finishing assemblies through tools for scaffolding contigs and close gaps. We also presented a case study that validated the efficacy of SIMBA to manage bacterial assemblies projects sequenced using Ion Torrent PGM. CONCLUSION: Besides to be a web tool for genome assembly, SIMBA is a complete genome assemblies project management system, which can be useful for managing of several projects in laboratories. SIMBA source code is available to download and install in local webservers at http://ufmg-simba.sourceforge.net .

Genome Sequence of Lactococcus lactis subsp. lactis NCDO 2118, a GABA-Producing Strain.

Lactococcus lactis subsp. lactis NCDO 2118 is a nondairy lactic acid bacterium, a xylose fermenter, and a gamma-aminobutyric acid (GABA) producer isolated from frozen peas. Here, we report the complete genome sequence of L. lactis NCDO 2118, a strain with probiotic potential activity.

The influence of sex and estrous cycle on QTL for emotionality and ethanol consumption.

The inbred rat strains Lewis (LEW) and Spontaneously Hypertensive Rats (SHR) differ with respect to several emotionality- and ethanol intake-related behaviors, one of which (inner locomotion in the open field; OF) is strongly influenced by a locus (Anxrr16) on chromosome (Chr) 4. We aimed to further investigate the influence of Chr 4 on these behaviors and to evaluate the role of the estrous cycle in QTL expression. LEW females and SHR males were intercrossed to produce F1 and F2 rats (96-97/sex), which were then tested in the OF, light-dark box (LDB), forced swimming test (FST), and an ethanol consumption procedure (ECP). In addition, another group of 96 F2 females were tested in the OF and LDB according to their estrous cycle phase. All animals were genotyped for microsatellite markers located on Chr 4 and two QTL analyses were performed. A factor analysis of the F2 population produced five factors reflecting different behavioral dimensions. QTL analysis revealed five significant loci in males, some of which with pleiotropic effects on behaviors measured in the OF, LDB, and ECP. The second QTL analysis revealed two significant loci in females in diestrous-proestrous and one in females in estrous-metestrous that influence behaviors in the OF and LDB. Results revealed that Anxrr16 and four other new QTL influence emotionality- and ethanol-related behaviors in male rats, whereas Anxrr16 attained suggestive levels only in females in diestrous-proestrous, which raises the need for taking into account factors related to the sex and estrous cycle in behavioral QTL analysis.