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[This corrects the article DOI: 10.3389/fgene.2023.1209416.].
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This perspective highlights the potential of individualized networks as a novel strategy for studying complex diseases through patient stratification, enabling advancements in precision medicine. We emphasize the impact of interpatient heterogeneity resulting from genetic and environmental factors and discuss how individualized networks improve our ability to develop treatments and enhance diagnostics. Integrating system biology, combining multimodal information such as genomic and clinical data has reached a tipping point, allowing the inference of biological networks at a single-individual resolution. This approach generates a specific biological network per sample, representing the individual from which the sample originated. The availability of individualized networks enables applications in personalized medicine, such as identifying malfunctions and selecting tailored treatments. In essence, reliable, individualized networks can expedite research progress in understanding drug response variability by modeling heterogeneity among individuals and enabling the personalized selection of pharmacological targets for treatment. Therefore, developing diverse and cost-effective approaches for generating these networks is crucial for widespread application in clinical services.
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Genome analysis of Bacillus safensis RP10, a strain from the soil of Atacama Desert in northern Chile, reflects a bacterium adapted to live in soil containing high levels of heavy metals, high salt conditions, and low carbon and energy sources.
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ABSTRACT In this report, we present a draft genome of 2,886,173 bp of an Exiguobacterium aurantiacum strain PN47 isolate from the sediment of a saline pond named "Salar del Huasco" in the Altiplano in the North of Chile. Strain PN47 encodes adaptive characteristics enabling survival in extreme environmental conditions of high heavy metal and salt concentrations and high alkalinity.
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Bacillaceae/isolamento & purificação , Bacillaceae/genética , Lagoas/microbiologia , Genoma Bacteriano , Filogenia , Bacillaceae/classificação , Bacillaceae/metabolismo , DNA Bacteriano/genética , Sequência de Bases , Cloreto de Sódio/análise , Cloreto de Sódio/metabolismo , Lagoas/química , Chile , Metais Pesados/análise , Metais Pesados/metabolismoRESUMO
In this report, we present a draft genome of 2,886,173 bp of an Exiguobacterium aurantiacum strain PN47 isolate from the sediment of a saline pond named Salar del Huasco in the Altiplano in the North of Chile. Strain PN47 encodes adaptive characteristics enabling survival in extreme environmental conditions of high heavy metal and salt concentrations and high alkalinity.(AU)
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Bacillaceae/genética , Metais Pesados , Alcalinidade da Água , Arsênio , Genoma Bacteriano , ChileRESUMO
In this report, we present a draft genome of 2,886,173bp of an Exiguobacterium aurantiacum strain PN47 isolate from the sediment of a saline pond named "Salar del Huasco" in the Altiplano in the North of Chile. Strain PN47 encodes adaptive characteristics enabling survival in extreme environmental conditions of high heavy metal and salt concentrations and high alkalinity.
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Bacillaceae/genética , Bacillaceae/isolamento & purificação , Genoma Bacteriano , Lagoas/microbiologia , Bacillaceae/classificação , Bacillaceae/metabolismo , Sequência de Bases , Chile , DNA Bacteriano/genética , Metais Pesados/análise , Metais Pesados/metabolismo , Filogenia , Lagoas/química , Cloreto de Sódio/análise , Cloreto de Sódio/metabolismoRESUMO
BACKGROUND: Acidithiobacillus ferrooxidans is a major participant in consortia of microorganisms used for the industrial recovery of copper (bioleaching or biomining). It is a chemolithoautrophic, gamma-proteobacterium using energy from the oxidation of iron- and sulfur-containing minerals for growth. It thrives at extremely low pH (pH 1-2) and fixes both carbon and nitrogen from the atmosphere. It solubilizes copper and other metals from rocks and plays an important role in nutrient and metal biogeochemical cycling in acid environments. The lack of a well-developed system for genetic manipulation has prevented thorough exploration of its physiology. Also, confusion has been caused by prior metabolic models constructed based upon the examination of multiple, and sometimes distantly related, strains of the microorganism. RESULTS: The genome of the type strain A. ferrooxidans ATCC 23270 was sequenced and annotated to identify general features and provide a framework for in silico metabolic reconstruction. Earlier models of iron and sulfur oxidation, biofilm formation, quorum sensing, inorganic ion uptake, and amino acid metabolism are confirmed and extended. Initial models are presented for central carbon metabolism, anaerobic metabolism (including sulfur reduction, hydrogen metabolism and nitrogen fixation), stress responses, DNA repair, and metal and toxic compound fluxes. CONCLUSION: Bioinformatics analysis provides a valuable platform for gene discovery and functional prediction that helps explain the activity of A. ferrooxidans in industrial bioleaching and its role as a primary producer in acidic environments. An analysis of the genome of the type strain provides a coherent view of its gene content and metabolic potential.
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Acidithiobacillus/genética , Acidithiobacillus/metabolismo , Genoma Bacteriano , Biologia Computacional , Genes Bacterianos , Microbiologia Industrial , Dados de Sequência Molecular , Família MultigênicaRESUMO
AlterORF is a searchable database that contains information regarding alternate open reading frames (ORFs) for over 1.5 million genes in 481 prokaryotic genomes. The objective of the database is to provide a platform for improving genome annotation and to serve as an aid for the identification of prokaryotic genes that potentially encode proteins in more than one reading frame. The AlterORF Database can be accessed through a web interface at www.alterorf.cl.
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Bases de Dados de Ácidos Nucleicos , Genômica , Fases de Leitura Aberta , Genoma Arqueal , Genoma Bacteriano , Internet , Proteínas/genética , Interface Usuário-ComputadorRESUMO
The gamma-proteobacterium Acidithiobacillus ferrooxidans lives in extremely acidic conditions (pH 2) and, unlike most organisms, is confronted with an abundant supply of soluble iron. It is also unusual in that it oxidizes iron as an energy source. Consequently, it faces the challenging dual problems of (i) maintaining intracellular iron homeostasis when confronted with extremely high environmental loads of iron and (ii) of regulating the use of iron both as an energy source and as a metabolic micronutrient. A combined bioinformatic and experimental approach was undertaken to identify Fur regulatory sites in the genome of A. ferrooxidans and to gain insight into the constitution of its Fur regulon. Fur regulatory targets associated with a variety of cellular functions including metal trafficking (e.g. feoPABC, tdr, tonBexbBD, copB, cdf), utilization (e.g. fdx, nif), transcriptional regulation (e.g. phoB, irr, iscR) and redox balance (grx, trx, gst) were identified. Selected predicted Fur regulatory sites were confirmed by FURTA, EMSA and in vitro transcription analyses. This study provides the first model for a Fur-binding site consensus sequence in an acidophilic iron-oxidizing microorganism and lays the foundation for future studies aimed at deepening our understanding of the regulatory networks that control iron uptake, homeostasis and oxidation in extreme acidophiles.