Brian C. Sanders

Ferromanganese nodules from the Clarion-Clipperton Zone (CCZ) located in the eastern Pacific Ocean between Hawaii and Mexico are enriched in a variety of critical metals. Understanding the spatial distribution of different metals, their partitioning between mineral phases, and pore-size distributions within the nodules can provide helpful insights into their formation mechanism. Here, we used a suite of techniques sensitive to the chemistry and texture of the nodule, including laser ablation–inductively coupled plasma–time-of-flight–mass spectrometry (LA-ICP-TOF-MS), Raman spectroscopy, scanning electron microscopy, and X-ray microtomography, to characterize key aspects of a single nodule from the Clarion-Clipperton Zone collected in the 1970s. We observed that parts of the nodules exhibited stratified zones enriched in cobalt (Co), nickel (Ni), copper (Cu), and rare earth elements (REEs) and found that Co, Ni, and Cu are spatially correlated with the distribution of the Mn-rich mineral phases. We also observed a stronger association of Ce and Co with other light REEs compared with heavier REEs. Within the porous rim of the nodule, micron-sized REE-enriched zones were detected, which are surrounded by Si- and Al-bearing phases and are not associated with phosphate phases. The results are consistent with alternating hydrogenetic and diagenetic growth conditions across part of the nodule and reveal heterogeneous REE distributions both within Mn-rich minerals and within distinct, likely inclusion-related phases.

Automated detection of features in cryogenic electron microscopy (cryoEM) micrographs is often the first step for quantitative downstream analysis. However, existing tools are often highly specialized for globular proteins, require good templates, or are built upon a large set of labeled images for training. For many non-biological cryoEM datasets labeled training data are unavailable, and samples are not optimized for automated analysis. Here we present CryoBlob, an open-source Python package for feature detection in low-SNR cryo-EM images. CryoBlob is implemented in JAX to allow for GPU acceleration and automatic differentiation during image analysis. The software brings together Laplacian-of-Gaussian blob detection alongside ridge, watershed, and Hessian-based methods to capture circular features, elongated structures, and overlapping objects in a single workflow. The package includes runtime parameter checks via Pydantic, handles large datasets with memory-aware batching, and reads/writes MRC and other common electron microscopy file types directly. In practice, this makes it useful both for quick sample screening and for more detailed quantitative or automated analysis pipelines.

The presence of pendant cationic functional groups in group 7 fac -tricarbonyl complexes produces unusual axial-halide substitution reactivity. The effects of the metal, axial halide, and solvent on the ligand substitution equilibrium are presented.

Monolignol-derived dimers containing β–β linkages are synthesized by vascular plants and can be released during lignin depolymerization. In this work, we isolated a bacterium, Novosphingobium rhizosphaerae LY, that grows with the β–β lignan (+)-pinoresinol as a sole growth substrate. Sequence analysis suggested that this strain encodes a broad range of pathways for assimilation of aromatic monomers as well as one enzyme implicated in pinoresinol catabolism but lacks other known pathways for aromatic dimer catabolism. We constructed a genome-wide barcoded transposon library and identified genes required for pinoresinol catabolism. Using feeding studies, compound isolation, targeted synthesis, and analysis of purified enzymes, we elucidated the biochemical intermediates and reaction pathway involved in pinoresinol catabolism. We demonstrated that the first enzymatic reaction is the reductive cleavage of a furan ring in (±)-pinoresinol with retention of configuration to yield lariciresinol. We additionally confirmed that the final pathway enzyme, PinU, is related to lignostilbene dioxygenases and oxidatively cleaves a diguaiacylbutadiene intermediate to yield vanillin and coniferaldehyde. Finally, based on the enzyme characterization, we demonstrated that the strain can grow with a second β–β lignan, (–)-syringaresinol, as a sole growth substrate. In combination, these results demonstrate a new biocatalytic route for transforming a widely occurring group of plant phenylpropanoid natural products. IMPORTANCE: Plants synthesize a variety of aromatic phenylpropanoid compounds containing β–β linkages, including lignin, a major structural polymeric component of the vascular plant cell wall, and lignans, biochemically related secondary metabolites with a wide range of bioactivities. Although microbial catabolic pathways have been described for dimeric phenylpropanoids featuring other interunit linkages, relatively little is known about pathways for catabolism of β–β-linked compounds. In this work, we isolated a Novosphingobium strain capable of degrading the β–β-linked lignan (+)-pinoresinol and elucidated the catabolic pathway. Understanding how bacteria catabolize β–β-linked compounds provides a basis for new biocatalytic transformations of lignans and oligolignols and has the potential to improve bacterial lignin valorization.

A microextraction (ME) sampling system, paired with inductively coupled plasma-mass spectrometry (ICP-MS), was employed to spatially analyze proteins tagged with lanthanum (La), gadolinium (Gd), or terbium (Tb) on the surface of western blot paper.

This work describes an analytical procedure, single particle-inductively coupled plasma-time-of-flight-mass spectrometry (SP-ICP-TOF-MS), that was developed to determine the platinum binding efficiency of protein-coated magnetic microparticles. SP-ICP-TOF-MS is advantageous due to its ability to quasi-simultaneously detect all nuclides (⁷Li–²⁴²Pu), allowing for both platinum and iron (composition of magnetic microparticles) to be measured concurrently. This method subsequently allows for the differentiation between bound and unbound platinum. The 1 μm magnetic microparticles were fully characterized for their iron concentration, particle concentration, and trace element composition by bulk digestion-ICP-MS and SP-ICP-TOF-MS. The results of both approaches agreed with the certificate values. Using the single particle methodology the platinum loading was quantified to be to 0.18 ± 0.02 fg per particle and 0.32 ± 0.02 fg per particle, for the streptavidin-coated and azurin-coated microparticles, respectively. Both streptavidin-coated and the azurin-coated microparticles had a particle–platinum association of >65%. Platinum bound samples were also analyzed via bulk digestion-based ICP-MS. The bulk ICP-MS results overestimated platinum loading due to free platinum in the samples. This highlights the importance of single particle analysis for a closer inspection of platinum binding performance. The SP-ICP-TOF-MS approach offers advantages over typical bulk digestion methods by eliminating laborious sample preparation, enabling differentiation between bound/unbound platinum in a solution, and quantification of platinum on a particle-by-particle basis. The procedure presented here enables quantification of metal content per particle, which could be broadly implemented for other single particle applications.

Direct-acting antivirals are needed to combat coronavirus disease 2019 (COVID-19), which is caused by severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2). The papain-like protease (PLpro) domain of Nsp3 from SARS-CoV-2 is essential for viral replication. In addition, PLpro dysregulates the host immune response by cleaving ubiquitin and interferon-stimulated gene 15 protein from host proteins. As a result, PLpro is a promising target for inhibition by small-molecule therapeutics. Here we design a series of covalent inhibitors by introducing a peptidomimetic linker and reactive electrophile onto analogs of the noncovalent PLpro inhibitor GRL0617. The most potent compound inhibits PLpro with k_inact/K_I = 9,600 M⁻¹ s⁻¹, achieves sub-μM EC₅₀ values against three SARS-CoV-2 variants in mammalian cell lines, and does not inhibit a panel of human deubiquitinases (DUBs) at >30 μM concentrations of inhibitor. An X-ray co-crystal structure of the compound bound to PLpro validates our design strategy and establishes the molecular basis for covalent inhibition and selectivity against structurally similar human DUBs. These findings present an opportunity for further development of covalent PLpro inhibitors.

Direct-acting antivirals are needed to combat coronavirus disease 2019 (COVID-19), which is caused by severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2). The papain-like protease (PLpro) domain of Nsp3 from SARS-CoV-2 is essential for viral replication. In addition, PLpro dysregulates the host immune response by cleaving ubiquitin and interferon-stimulated gene 15 protein (ISG15) from host proteins. As a result, PLpro is a promising target for inhibition by small-molecule therapeutics. Here we have designed a series of covalent inhibitors by introducing a peptidomimetic linker and reactive electrophile onto analogs of the noncovalent PLpro inhibitor GRL0617. The most potent compound inhibited PLpro with k_inact/K_I = 10,000 M^− 1 s^− 1, achieved sub-µM EC₅₀ values against three SARS-CoV-2 variants in mammalian cell lines, and did not inhibit a panel of human deubiquitinases at > 30 µM concentrations of inhibitor. An X-ray co-crystal structure of the compound bound to PLpro validated our design strategy and established the molecular basis for covalent inhibition and selectivity against structurally similar human DUBs. These findings present an opportunity for further development of covalent PLpro inhibitors.

Direct-acting antivirals are needed to combat coronavirus disease 2019 (COVID-19), which is caused by severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2). The papain-like protease (PLpro) domain of Nsp3 from SARS-CoV-2 is essential for viral replication. In addition, PLpro dysregulates the host immune response by cleaving ubiquitin and interferon-stimulated gene 15 protein (ISG15) from host proteins. As a result, PLpro is a promising target for inhibition by small-molecule therapeutics. Here we have designed a series of covalent inhibitors by introducing a peptidomimetic linker and reactive electrophile onto analogs of the noncovalent PLpro inhibitor GRL0617. The most potent compound inhibited PLpro with k_inact/K_I = 10,000 M^− 1 s^− 1, achieved sub-µM EC₅₀ values against three SARS-CoV-2 variants in mammalian cell lines, and did not inhibit a panel of human deubiquitinases at > 30 µM concentrations of inhibitor. An X-ray co-crystal structure of the compound bound to PLpro validated our design strategy and established the molecular basis for covalent inhibition and selectivity against structurally similar human DUBs. These findings present an opportunity for further development of covalent PLpro inhibitors.