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- Omics Biology in Diagnosis of Diseases: Towards Empowering Genomic Medicine from an Evolutionary PerspectivePublication . Maldonado, Emanuel; Khan, ImranIn this section, we reintroduce the original aims and scope of the Special Issue entitled “Omics Biology in Diagnosis of Diseases: Advances in Bioinformatics and Data Analyses”, enabling readers to find an appropriate framing for the remainder of the present closing editorial. Readers aware of this can skip this section. [...]
- Natural Transformation as a Mechanism of Horizontal Gene Transfer in Aliarcobacter butzleriPublication . Bonifácio, Marina; Mateus, Cristiana; Alves, Ana R.; Maldonado, Emanuel; Duarte, Ana Paula; Domingues, Fernanda; Oleastro, Mónica; Ferreira, SusanaAliarcobacter butzleri is an emergent enteropathogen, showing high genetic diversity, which likely contributes to its adaptive capacity to different environments. Whether natural transformation can be a mechanism that generates genetic diversity in A. butzleri is still unknown. In the present study, we aimed to establish if A. butzleri is naturally competent for transformation and to investigate the factors influencing this process. Two different transformation procedures were tested using exogenous and isogenic DNA containing antibiotic resistance markers, and different external conditions influencing the process were evaluated. The highest number of transformable A. butzleri strains were obtained with the agar transformation method when compared to the biphasic system (65% versus 47%). A. butzleri was able to uptake isogenic chromosomal DNA at different growth phases, and the competence state was maintained from the exponential to the stationary phases. Overall, the optimal conditions for transformation with the biphasic system were the use of 1 µg of isogenic DNA and incubation at 30 ◦C under a microaerobic atmosphere, resulting in a transformation frequency ~8 × 10−6 transformants/CFU. We also observed that A. butzleri favored the transformation with the genetic material of its own strain/species, with the DNA incorporation process occurring promptly after the addition of genomic material. In addition, we observed that A. butzleri strains could exchange genetic material in co-culture assays. The presence of homologs of well-known genes involved in the competence in the A. butzleri genome corroborates the natural competence of this species. In conclusion, our results show that A. butzleri is a naturally transformable species, suggesting that horizontal gene transfer mediated by natural transformation is one of the processes contributing to its genetic diversity. In addition, natural transformation can be used as a tool for genetic studies of this species.
- Computational Resources and Infrastructures for a Novel Bioinformatics Laboratory: A Case StudyPublication . Maldonado, Emanuel Filipe Escaleira ; Lemos, Manuel; Manoj, Gupta; Dennis, DouroumisIntroduction: Bioinformatics is a relatively recent multidisciplinary research field continuously offering novel opportunities. Although many researchers are actively working in/with bioinformatics, some research centers still face difficulties in hiring bioinformaticians and establishing the appropriate (first) bioinformatics infrastructures and computational resources. In our research center, we started from scratch and established initial bioinformatics infrastructures for common use and also for the specific case of precision/personalized medicine. Case description: Here, we report a case study reflecting our specific needs and circumstances during the implementation of a novel bioinformatics laboratory. This involved the preparation of rooms, computer networks, computational resources novel designs, and upgrades to existing designs. Moreover, this work involved people from diverse areas and institutions, such as companies, institutional projects, informatics, and technical infrastructures services. Discussion and evaluation: The work resulted in the implementation of four novel designs dedicated to genomic medicine and in the adaptation of two existing designs dedicated to common use located in the dry-lab room. This is not an accurate and objective work, as it often depends on the available computer hardware and the target bioinformatics field(s). The four novel designs offered substantial improvements when compared to the upgraded designs, additionally corroborated by performance evaluations, which resulted in an overall highest performance of the novel designs. Conclusions: We present work that was developed over two years until completion with functioning infrastructure. This project enabled us to learn many novel aspects not only related to redundant disk technologies, but also related to computer networks, hardware, storage-management operating systems, file systems, performance evaluation, and also in the management of services. Moreover, additional equipment will be important to maintain and expand the potential and reliability of the bioinformatics laboratory. We hope that this work can be helpful for other researchers seeking to design their bioinformatics equipment or laboratories.