Biology subjects

Stein, A. M.

Publications and source records attributed to Stein, A. M..

3 recordsLinked to original sources

bioRxiv2026

The distribution of particle-associated Prochlorococcus across the global oceans

The picocyanobacterium Prochlorococcus is a fundamental contributor to ocean primary productivity. While its free-living population has been extensively studied, primarily using flow cytometric analyses, the size and distribution of its particle-associated population is not well understood. Using filter fractionated samples from cruises in the Pacific Ocean, Atlantic Ocean, and Mediterranean Sea, we generated metagenomic data using internal standards, yielding absolute genome equivalent counts of Prochlorococcus cells in different size fractions. We used these data to model a relationship between relative and absolute genome equivalent counts, yielding a correction factor that we validated using published datasets. We then applied the correction factor to size-fractionated global metagenomic data from the TARA Oceans Project, which has widespread Prochlorococcus cells in size fractions >1.6 m throughout the transects, to calculate the fraction of the total Prochlorococcus population in large size fractions. The ''particle-associated'' population fraction increased with net primary productivity. Dissolved inorganic carbon was also directly correlated with increased particle association, which, combined with other evidence, could indicate an association with upwelling. We also examined the relationship between particle-associated population and carbon export at 150 m by incorporating published estimates of carbon flux based on TARA optical scattering data. This study highlights the potential importance of particle-associated Prochlorococcus to carbon flux in marine ecosystems and offers a way to convert relative to absolute genome equivalents of microorganisms in archival metagenomic datasets.

ecology↗

bioRxiv2025

Crystal structure of the Legionella pneumophila effector SidL (Lpg0437) in complex with its metaeffector LegA11 (Lpg0436)

Legionella pneumophila is an opportunistic human pathogen that causes atypical pneumonia called Legionnaires Disease. To replicate within host cells, L. pneumophila injects up to 330 effector proteins into the host cytosol via a Dot/Icm type IV secretion system. Several effectors, called metaeffectors, regulate the activity of other effectors within infected host cells through direct protein-protein interactions. LegA11 (AnkJ/Lpg0436) has been identified as a putative metaeffector of SidL (Ceg14/Lpg0437), one of eight L. pneumophila effectors that inhibit host mRNA translation. LegA11 binds and suppresses SidL enzymatic activity, but the molecular basis of this regulation and impact on mRNA translation are unknown. Here, we present the crystal structure of SidL in complex with LegA11 to a resolution of 2.4 [A], revealing a high-affinity 1:1 complex with an extensive interaction interface of [~]2300 [A]{superscript 2}. Using isothermal titration calorimetry, we determined a dissociation constant of 1.8 nM. In vitro translation assays demonstrate that SidL inhibits mRNA translation, and this activity is completely suppressed by LegA11. Mutagenesis of key interface residues in LegA11 disrupts complex formation and abolishes its metaeffector activity, confirming that LegA11 regulates SidL through direct protein-protein interaction. These findings establish LegA11 as a bona fide metaeffector that contributes to suppression of host mRNA translation by L. pneumophila.

microbiology↗

bioRxiv2018

Guiding dose selection of monoclonal antibodies using a new parameter (AFTIR) for characterizing ligand binding systems

Guiding the dose selection for monoclonal antibody oncology drugs is often done using methods for predicting the receptor occupancy of the drug in the tumor. In this manuscript, previous work on characterizing target inhibition at steady state using the AFIR metric [1] is extended to include a \"target-tissue\" compartment and the shedding of membrane-bound targets. A new potency metric AFTIR (Averarge Free Tissue target to Initial target ratio at steady state) is derived, and it depends on only four key quantities: the equilibrium binding constant, the fold-change in target expression at steady state after binding to drug, the biodistribution of target from circulation to target tissue, and the average drug concentration in circulation. The AFTIR metric is useful for guiding dose selection, for efficiently performing sensitivity analyses, and for building intuition for more complex target mediated drug disposition models. In particular, reducing the complex, physiological model to four key parameters needed to predict target inhibition helps to highlight specific parameters that are the most important to estimate in future experiments to guide drug development.\n\nGraphical Abstract\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=145 SRC=\"FIGDIR/small/432500_fig1.gif\" ALT=\"Figure 1\">\nView larger version (30K):\norg.highwire.dtl.DTLVardef@6895d7org.highwire.dtl.DTLVardef@4566e0org.highwire.dtl.DTLVardef@6515e8org.highwire.dtl.DTLVardef@8168ea_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFig. 1C_FLOATNO Graphical Abstract\n\nC_FIG

pharmacology and toxicology↗