Draft genome sequence of three hydrocarbon-degrading Pseudomonadota strains isolated from an abandoned century-old oil exploration well

We present genome sequences of three Pseudomonadota strains isolated from an abandoned century-old oil exploration well. A Pseudomonas sp. genome showed a size of 5,378,420 bp, while Acinetobacter genomes sized 3,522,593 and 3,864,311 bp. Genomes included catabolic genes for benzoate, 4-hydroxybenzoate, salicylate, vanillate, indoleacetate, anthranilate, n-alkanes, 4-hydroxyphenylacetate, phenylacetate, among others

Classical resolution of black hole singularities via wormholes

In certain extensions of General Relativity, wormholes generated by spherically symmetric electric fields can resolve black hole singularities without necessarily removing curvature divergences. This is shown by studying geodesic completeness, the behavior of time-like congruences going through the divergent region, and by means of scattering of waves off the wormhole. This provides an example of the logical independence between curvature divergences and space-time singularities, concepts very often identified with each other in the literature.ns of curvature divergences in the context of space-time singularities.Comment: 6 pages, 4 figures; several improvements in main body and abstract; final version to appear in Eur. Phys. J.

Special Issue: Diversity of Extremophiles in Time and Space

Extreme environments are fascinating ecosystems that have allowed us to increase our knowledge about the evolutionary processes of life [1], develop new biotechnological applications (e.g., industrial applications of lipases [2], and thermostable DNA Polymerases in PCR tests [3]) and establish some fundamental concepts about the origins of life and the search for life in the Universe [1]. Despite the fact that research on the living beings that inhabit these extreme environments (i.e., extremophiles) began more than five decades ago with the pioneering works of Thomas D. Brock [4], nowadays, we still have a lot to learn about microbial diversity, and especially about the metabolism and biochemistry of these microorganisms; therefore, the study of extremophiles, extremozymes and their biotechnological potential remains a hot topic.Universidad de Costa Rica/[809-B6-524]/UCR/Costa RicaEuropean Union’s Horizon/[892961]/EU/Unión EuropeaUCR::Vicerrectoría de Investigación::Unidades de Investigación::Ciencias Básicas::Centro de Investigaciones en Productos Naturales (CIPRONA

Exploring environmental intra-species diversity through non-redundant pangenome assemblies

At the genome level, microorganisms are highly adaptable both in terms of allele and gene composition. Such heritable traits emerge in response to different environmental niches and can have a profound influence on microbial community dynamics. As a consequence, any individual genome or population will contain merely a fraction of the total genetic diversity of any operationally defined "species", whose ecological potential can thus be only fully understood by studying all of their genomes and the genes therein. This concept, known as the pangenome, is valuable for studying microbial ecology and evolution, as it partitions genomes into core (present in all the genomes from a species, and responsible for housekeeping and species-level niche adaptation among others) and accessory regions (present only in some, and responsible for intra-species differentiation). Here we present SuperPang, an algorithm producing pangenome assemblies from a set of input genomes of varying quality, including metagenome-assembled genomes (MAGs). SuperPang runs in linear time and its results are complete, non-redundant, preserve gene ordering and contain both coding and non-coding regions. Our approach provides a modular view of the pangenome, identifying operons and genomic islands, and allowing to track their prevalence in different populations. We illustrate this by analysing intra-species diversity in Polynucleobacter, a bacterial genus ubiquitous in freshwater ecosystems, characterized by their streamlined genomes and their ecological versatility. We show how SuperPang facilitates the simultaneous analysis of allelic and gene content variation under different environmental pressures, allowing us to study the drivers of microbial diversification at unprecedented resolution

The emergence of interstellar molecular complexity explained by interacting networks

Recent years have witnessed the detection of an increasing number of complex organicmolecules in interstellar space, some of them being of prebiotic interest. Disentanglingthe origin of interstellar prebiotic chemistry and its connection to biochemistry andultimately, to biology is an enormously challenging scientific goal where the applicationof complexity theory and network science has not been fully exploited. Encouragedby this idea, we present a theoretical and computational framework to model theevolution of simple networked structures toward complexity. In our environment,complex networks represent simplified chemical compounds and interact optimizing thedynamical importance of their nodes. We describe the emergence of a transition fromsimple networks toward complexity when the parameter representing the environmentreaches a critical value. Notably, although our system does not attempt to model the rulesof real chemistry nor is dependent on external input data, the results describe the emer-gence of complexity in the evolution of chemical diversity in the interstellar medium.Furthermore, they reveal an as yet unknown relationship between the abundances ofmolecules in dark clouds and the potential number of chemical reactions that yieldthem as products, supporting the ability of the conceptual framework presented here toshed light on real scenarios. Our work reinforces the notion that some of the propertiesthat condition the extremely complex journey from the chemistry in space to prebioticchemistry and finally, to life could show relatively simple and universal patterns

Application of Deadlock Risk Evaluation of Architectural Models

Software architectural evaluation is a key discipline used to identify, at early stages of a real-time system (RTS) development, the problems that may arise during its operation. Typical mechanisms supporting concurrency, such as semaphores, mutexes or monitors, usually lead to concurrency problems in execution time that are difficult to be identified, reproduced and solved. For this reason, it is crucial to understand the root causes of these problems and to provide support to identify and mitigate them at early stages of the system lifecycle. This paper aims to present the results of a research work oriented to the development of the tool called ‘Deadlock Risk Evaluation of Architectural Models’ (DREAM) to assess deadlock risk in architectural models of an RTS. A particular architectural style, Pipelines of Processes in Object-Oriented Architectures–UML (PPOOA) was used to represent platform-independent models of an RTS architecture supported by the PPOOA –Visio tool. We validated the technique presented here by using several case studies related to RTS development and comparing our results with those from other deadlock detection approaches, supported by different tools. Here we present two of these case studies, one related to avionics and the other to planetary exploration robotics. Copyright © 2011 John Wiley & Sons, Ltd