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1. NADH dehydrogenases drive inward electron transfer in Shewanella oneidensis MR ‐1

   https://doi.org/10.1111/1751-7915.14175  

   Tefft, Nicholas M. ; Ford, Kathryne ; TerAvest, Michaela A. ( November 2022 , Microbial Biotechnology)

   Shewanella oneidensisMR‐1 is a promising chassis organism for microbial electrosynthesis because it has a well‐defined biochemical pathway (the Mtr pathway) that can connect extracellular electrodes to respiratory electron carriers inside the cell. We previously found that the Mtr pathway can be used to transfer electrons from a cathode to intracellular electron carriers and drive reduction reactions. In this work, we hypothesized that native NADH dehydrogenases form an essential link between the Mtr pathway and NADH in the cytoplasm. To test this hypothesis, we compared the ability of various mutant strains to accept electrons from a cathode and transfer them to an NADH‐dependent reaction in the cytoplasm, reduction of acetoin to 2,3‐butanediol. We found that deletion of genes encoding NADH dehydrogenases from the genome blocked electron transfer from a cathode to NADH in the cytoplasm, preventing the conversion of acetoin to 2,3‐butanediol. However, electron transfer to fumarate was not blocked by the gene deletions, indicating that NADH dehydrogenase deletion specifically impacted NADH generation and did not cause a general defect in extracellular electron transfer. Proton motive force (PMF) is linked to the function of the NADH dehydrogenases. We added a protonophore to collapse PMF and observed that it blocked inward electron transfer to acetoin but not fumarate. Together these results indicate a link between the Mtr pathway and intracellular NADH. Future work to optimize microbial electrosynthesis inS. oneidensisMR‐1 should focus on optimizing flux through NADH dehydrogenases.

    

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2. RCSB Protein Data Bank: Celebrating 50 years of the PDB with new tools for understanding and visualizing biological macromolecules in 3D

   https://doi.org/10.1002/pro.4213  

   Burley, Stephen K. ; Bhikadiya, Charmi ; Bi, Chunxiao ; Bittrich, Sebastian ; Chen, Li ; Crichlow, Gregg V. ; Duarte, Jose M. ; Dutta, Shuchismita ; Fayazi, Maryam ; Feng, Zukang ; et al ( November 2021 , Protein Science)

   The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), funded by the US National Science Foundation, National Institutes of Health, and Department of Energy, has served structural biologists and Protein Data Bank (PDB) data consumers worldwide since 1999. RCSB PDB, a founding member of the Worldwide Protein Data Bank (wwPDB) partnership, is the US data center for the global PDB archive housing biomolecular structure data. RCSB PDB is also responsible for the security of PDB data, as the wwPDB‐designated Archive Keeper. Annually, RCSB PDB serves tens of thousands of three‐dimensional (3D) macromolecular structure data depositors (using macromolecular crystallography, nuclear magnetic resonance spectroscopy, electron microscopy, and micro‐electron diffraction) from all inhabited continents. RCSB PDB makes PDB data available from its research‐focusedRCSB.orgweb portal at no charge and without usage restrictions to millions of PDB data consumers working in every nation and territory worldwide. In addition, RCSB PDB operates an outreach and educationPDB101.RCSB.orgweb portal that was used by more than 800,000 educators, students, and members of the public during calendar year 2020. This invited Tools Issue contribution describes (i) how the archive is growing and evolving as new experimental methods generate ever larger and more complex biomolecular structures; (ii) the importance of data standards and data remediation in effective management of the archive and facile integration with more than 50 external data resources; and (iii) new tools and features for 3D structure analysis and visualization made available during the past yearviatheRCSB.orgweb portal.

    

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3. Atomic data calculations for Au i –Au iii and exploration in the application of collisional-radiative theory to laboratory and neutron star merger plasmas

   https://doi.org/10.1093/mnras/stab3285  

   McCann, Michael ; Bromley, S ; Loch, S D ; Ballance, C P ( December 2021 , Monthly Notices of the Royal Astronomical Society)

   ABSTRACT Neutron binary star mergers have long been proposed as sufficiently neutron rich environments that could support the synthesis of rapid neutron capture elements (r-process elements) such as gold. However, the literature reveals that beyond neutral and singly ionized systems, there is an incompleteness of atomic data for the remaining ion stages of importance for mergers. In this work, we report on relativistic atomic structure calculations for Au i–Au iii using the grasp0 codes. Comparisons to calculations using the Flexible Atomic Code suggest uncertainties on average of 9.2 per cent, 5.7 per cent, and 3.8 per cent for Au i–Au iii level energies. Agreement around ∼50 per cent is achieved between our computed A-values and those in the literature, where available. Using the grasp0 structure of Au i, we calculated electron-impact excitation rate coefficients and use a collisional-radiative model to explore the excitation dynamics and line ratio diagnostics possible in neutron star merger environments. We find that proper accounting of metastable populations is critical for extracting useful information from ultraviolet–visible line ratio diagnostics of Au i. As a test of our data, we applied our electron-impact data to study a gold hollow cathode spectrum in the literature and diagnosed the plasma conditions as Te = 3.1 ± 1.2 eV and $n_\textrm {e} = 2.7^{+1.3}_{-0.9}\times 10^{13}$ cm−3. 

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4. 3D reconstruction of murine mitochondria reveals changes in structure during aging linked to the MICOS complex

   https://doi.org/10.1111/acel.14009  

   Vue, Zer ; Garza‐Lopez, Edgar ; Neikirk, Kit ; Katti, Prasanna ; Vang, Larry ; Beasley, Heather ; Shao, Jianqiang ; Marshall, Andrea G. ; Crabtree, Amber ; Murphy, Alexandria C. ; et al ( November 2023 , Aging Cell)

   During aging, muscle gradually undergoes sarcopenia, the loss of function associated with loss of mass, strength, endurance, and oxidative capacity. However, the 3D structural alterations of mitochondria associated with aging in skeletal muscle and cardiac tissues are not well described. Although mitochondrial aging is associated with decreased mitochondrial capacity, the genes responsible for the morphological changes in mitochondria during aging are poorly characterized. We measured changes in mitochondrial morphology in aged murine gastrocnemius, soleus, and cardiac tissues using serial block‐face scanning electron microscopy and 3D reconstructions. We also used reverse transcriptase‐quantitative PCR, transmission electron microscopy quantification, Seahorse analysis, and metabolomics and lipidomics to measure changes in mitochondrial morphology and function after loss of mitochondria contact site and cristae organizing system (MICOS) complex genes,Chchd3,Chchd6, andMitofilin. We identified significant changes in mitochondrial size in aged murine gastrocnemius, soleus, and cardiac tissues. We found that both age‐related loss of the MICOS complex and knockouts of MICOS genes in mice altered mitochondrial morphology. Given the critical role of mitochondria in maintaining cellular metabolism, we characterized the metabolomes and lipidomes of young and aged mouse tissues, which showed profound alterations consistent with changes in membrane integrity, supporting our observations of age‐related changes in muscle tissues. We found a relationship between changes in the MICOS complex and aging. Thus, it is important to understand the mechanisms that underlie the tissue‐dependent 3D mitochondrial phenotypic changes that occur in aging and the evolutionary conservation of these mechanisms betweenDrosophilaand mammals.

    

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5. Direct cathodic electron uptake coupled to sulfate reduction by Desulfovibrio ferrophilus IS5 biofilms

   https://doi.org/10.1111/1462-2920.15235  

   McCully, Alexandra L. ; Spormann, Alfred M. ( September 2020 , Environmental Microbiology)

   Direct electron uptake is emerging as a key process for electron transfer in anaerobic microbial communities, both between species and from extracellular sources, such as zero‐valent iron (Fe⁰) or cathodic surfaces. In this study, we investigated cathodic electron uptake by Fe⁰‐corrodingDesulfovibrio ferrophilusIS5 and showed that electron uptake is dependent on direct cell contact via a biofilm on the cathode surface rather than through secreted intermediates. Induction of cathodic electron uptake by lactate‐starvedD. ferrophilusIS5 cells resulted in the expression of all components necessary for electron uptake; however, protein synthesis was required for full biofilm formation. Notably, proteinase K treatment uncoupled electron uptake from biofilm formation, likely through proteolytic degradation of proteinaceous components of the electron uptake machinery. We also showed that cathodic electron uptake is dependent on SO₄²⁻reduction. The insensitivity of Fe⁰corrosion to proteinase K treatment suggests that electron uptake from a cathode might involve different mechanism(s) than those involved in Fe⁰corrosion.

    

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