Minimal and hybrid hydrogenases are active from archaea.

Microbial hydrogen (H2) cycling underpins the diversity and functionality of diverse anoxic ecosystems. Among the three evolutionarily distinct hydrogenase superfamilies responsible, [FeFe] hydrogenases were thought to be restricted to bacteria and eukaryotes. Here, we show that anaerobic archaea encode diverse, active, and ancient lineages of [FeFe] hydrogenases through combining analysis of existing and new genomes with extensive biochemical experiments. [FeFe] hydrogenases are encoded by genomes of nine archaeal phyla and expressed by H2-producing Asgard archaeon cultures. We report an ultraminimal hydrogenase in DPANN archaea that binds the catalytic H-cluster and produces H2. Moreover, we identify and characterize remarkable hybrid complexes formed through the fusion of [FeFe] and [NiFe] hydrogenases in ten other archaeal orders. Phylogenetic analysis and structural modeling suggest a deep evolutionary history of hybrid hydrogenases. These findings reveal new metabolic adaptations of archaea, streamlined H2 catalysts for biotechnological development, and a surprisingly intertwined evolutionary history between the two major H2-metabolizing enzymes.

aCLImatise: automated generation of tool definitions for bioinformatics workflows.

SUMMARY: aCLImatise is a utility for automatically generating tool definitions compatible with bioinformatics workflow languages, by parsing command-line help output. aCLImatise also has an associated database called the aCLImatise Base Camp, which provides thousands of pre-computed tool definitions. AVAILABILITY AND IMPLEMENTATION: The latest aCLImatise source code is available within a GitHub organisation, under the GPL-3.0 license: https://github.com/aCLImatise. In particular, documentation for the aCLImatise Python package is available at https://aclimatise.github.io/CliHelpParser/, and the aCLImatise Base Camp is available at https://aclimatise.github.io/BaseCamp/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Localized Spin Dimers and Structural Distortions in the Hexagonal Perovskite Ba3CaMo2O9.

Extended solid-state materials based on the hexagonal perovskite framework are typified by close competition between localized magnetic interactions and quasi-molecular electronic states. Here, we report the structural and magnetic properties of the new six-layer hexagonal perovskite Ba3CaMo2O9. Neutron diffraction experiments, combined with magnetic susceptibility measurements, show that the Mo2O9 dimers retain localized character down to 5 K and adopt nonmagnetic spin-singlet ground states. This is in contrast to the recently reported Ba3SrMo2O9 analogue, in which the Mo2O9 dimers spontaneously separate into a mixture of localized and quasi-molecular ground states. Structural distortions in both Ba3CaMo2O9 and Ba3SrMo2O9 have been studied with the aid of distortion mode analyses to elucidate the coupling between the crystal lattice and electronic interactions in 6H Mo5+ hexagonal perovskites.

Trace gas oxidation sustains energy needs of a thermophilic archaeon at suboptimal temperatures.

Diverse aerobic bacteria use atmospheric hydrogen (H2) and carbon monoxide (CO) as energy sources to support growth and survival. Such trace gas oxidation is recognised as a globally significant process that serves as the main sink in the biogeochemical H2 cycle and sustains microbial biodiversity in oligotrophic ecosystems. However, it is unclear whether archaea can also use atmospheric H2. Here we show that a thermoacidophilic archaeon, Acidianus brierleyi (Thermoproteota), constitutively consumes H2 and CO to sub-atmospheric levels. Oxidation occurs across a wide range of temperatures (10 to 70 °C) and enhances ATP production during starvation-induced persistence under temperate conditions. The genome of A. brierleyi encodes a canonical CO dehydrogenase and four distinct [NiFe]-hydrogenases, which are differentially produced in response to electron donor and acceptor availability. Another archaeon, Metallosphaera sedula, can also oxidize atmospheric H2. Our results suggest that trace gas oxidation is a common trait of Sulfolobales archaea and may play a role in their survival and niche expansion, including during dispersal through temperate environments.

Bionitio: demonstrating and facilitating best practices for bioinformatics command-line software.

BACKGROUND: Bioinformatics software tools are often created ad hoc, frequently by people without extensive training in software development. In particular, for beginners, the barrier to entry in bioinformatics software development is high, especially if they want to adopt good programming practices. Even experienced developers do not always follow best practices. This results in the proliferation of poorer-quality bioinformatics software, leading to limited scalability and inefficient use of resources; lack of reproducibility, usability, adaptability, and interoperability; and erroneous or inaccurate results. FINDINGS: We have developed Bionitio, a tool that automates the process of starting new bioinformatics software projects following recommended best practices. With a single command, the user can create a new well-structured project in 1 of 12 programming languages. The resulting software is functional, carrying out a prototypical bioinformatics task, and thus serves as both a working example and a template for building new tools. Key features include command-line argument parsing, error handling, progress logging, defined exit status values, a test suite, a version number, standardized building and packaging, user documentation, code documentation, a standard open source software license, software revision control, and containerization. CONCLUSIONS: Bionitio serves as a learning aid for beginner-to-intermediate bioinformatics programmers and provides an excellent starting point for new projects. This helps developers adopt good programming practices from the beginning of a project and encourages high-quality tools to be developed more rapidly. This also benefits users because tools are more easily installed and consistent in their usage. Bionitio is released as open source software under the MIT License and is available at https://github.com/bionitio-team/bionitio.

Influence of Soft Drink Intake on the Salivary pH of Schoolchildren

Objective: To evaluate the influence of Coca-Cola® consumption on the salivary pH of 12-year old children. Material and Methods: The convenience sample was composed of forty-five 12-year old students of both genders from public schools of Itatiba, state of São Paulo, Brazil. Salivary pH was measured with pH colorimetric tape indicator (Merck). The reading of the colorimetric method was made by an experienced evaluator under uniform lighting conditions. The colorimetric tape was positioned in the back of the student's tongue, which remained with the mouth shut for 30 Seconds. For control, the first measurement (T0) was performed before the intake of the soft drink (baseline pH). Subsequently, students were instructed to slowly drink 100 ml of Coca-Cola® using a plastic disposable cup. Immediately after ingestion, the pH was measured again with the colorimetric tape (t1). The oral pH values were also measured 5 minutes (t2), 10 minutes (t3) and 15 minutes (t4) after the soft drink intake, keeping the tape positioning always the same in all measurements. The statistical SAS software was used for data analysis. Comparisons of oral pH values at different times were performed by the Tukey-Kramer test adopting 5% significance level. Results: Immediately after soft drink intake, the salivary pH significantly decreased (pH = 6.26) (p <0.05) compared to baseline (pH = 7.23) (p <0.05). Fifteen minutes after ingestion, although an increase in the pH was observed (pH = 6.64), it had not yet returned to baseline (T0) (p <0.05). Conclusion: Coca-Cola® intake caused a significant reduction in salivary pH, without, however, reaching critical pH for enamel demineralization.