Biology subjects

Bradley, A. S.

Publications and source records attributed to Bradley, A. S..

4 recordsLinked to original sources

bioRxiv2026

Quantifying biomarker ambiguity using metabolic network analysis

Molecular biomarkers preserved in rocks provide evidence about ancient life but interpreting them requires inference through multiple stages of information loss arising from phylogenetic, biosynthetic, and diagenetic ambiguity. However, biomarker specificity is typically assessed qualitatively rather than quantitatively. Here we formalize biosynthetic ambiguity as entropy over metabolic networks. We introduce three metrics that quantify pathway-level information content: retrobiosynthetic complexity ({psi}), normalized branch depth ({lambda}), and fraction shared ({sigma}). Analysis of 9,140 MetaCyc metabolites defines a three-dimensional specificity space for biomarker evaluation. Only 13% of multi-pathway compounds exhibited low complexity, distal divergence, and high pathway consensus. Lipid biomarkers span this specificity space heterogeneously: hopanoids cluster near the high-specificity region while sterols occupy intermediate territory. Diagnostic quality and lipophilicity are approximately independent, so the constraint on molecular paleontology is the limited chemical diversity among preservable compound classes rather than their biosynthetic properties. This framework supports probabilistic biomarker interpretation by explicitly incorporating biosynthetic, phylogenetic, and diagenetic constraints.

bioinformatics↗

bioRxiv2023

Energy flux couples sulfur isotope fractionation to proteomic and metabolite profiles in Desulfovibrio vulgaris

Microbial sulfate reduction is central to the global carbon cycle and the redox evolution of Earths surface. Tracking the activity of sulfate reducing microorganisms over space and time relies on a nuanced understanding of stable sulfur isotope fractionation in the context of the biochemical machinery of the metabolism. Here we link the magnitude of stable sulfur isotopic fractionation to proteomic and metabolite profiles under different cellular energetic regimes. When energy availability is limited, cell specific sulfate respiration rates and net sulfur isotope fractionation inversely co-vary. Beyond net S isotope fractionation values, we also quantified shifts in protein expression, abundances and isotopic composition of intracellular S metabolites, and lipid structures and lipid/water H isotope fractionation values. These coupled approaches reveal which protein abundances shift directly as a function of energy flux, those that vary minimally, and those that may vary independent of energy flux and likely do not contribute to shifts in S-isotope fractionation. By coupling the bulk S-isotope observations with quantitative proteomics, we provide novel constraints for metabolic isotope models. Together, these results lay the foundation for more predictive metabolic fractionation models, alongside interpretations of environmental sulfur and sulfate reducer lipid-H isotope data.

microbiology↗

bioRxiv2017

Hydrogen Isotope Composition Of Thermoanaerobacterium saccharolyticum Lipids: Comparing Wild Type To A nfn- Transhydrogenase Mutant

AbstractThe 2H/1H ratio in microbial fatty acids can record information about the energy metabolism of microbes and about the isotopic composition of environmental water. However, the mechanisms involved in the fractionation of hydrogen isotopes between water and lipid are not fully resolved. We provide data aimed at understanding this fractionation in the Gram-positive obligately thermophilic anaerobe, Thermoanaerobacterium saccharolyticum, by comparing a wild-type strain to a deletion mutant in which the nfnAB genes encoding electron-bifurcating transhydrogenase have been removed. The wild-type strain showed faster growth rates and larger overall fractionation [Formula] than the mutant strain [Formula]. The overall trend in growth rate and fractionation, along with the isotopic ordering of individual lipids, is consistent with results reported for the Gram-negative sulfate reducer, Desulfovibrio alaskensis G20.

microbiology↗

bioRxiv2017

Heritability of the structures and 13C fractionation in tomato leaf wax alkanes: a genetic model system to inform paleoenvironmental reconstructions

Leaf wax n-alkanes are broadly used to reconstruct paleoenvironmental information. However, the utility of the n-alkane paleoclimate proxy is modulated by the extent to which genetic as well as environmental factors influence the structural and isotopic variability of leaf waxes. In paleoclimate applications, there is an implicit assumption that most variation of leaf wax traits through a time series can be attributed to environmental change and that biological sources of variability within plant communities are small. For example, changes in hydrology affect the {delta}2 H of waxes though rainwater and the {delta}13C of leaf waxes by changing plant communities (i.e., C3 versus C4 input). Here we test the assumption of little genetic control over 5 C variation of leaf wax by presenting the results of an experimental greenhouse growth study in which we estimate the role of genetic variability on structural and isotopic leaf wax traits in a set of 76 introgression lines (ILs) between two interfertile Solanum (tomato) species: S. lycopersicum cv M82 (hereafter cv M82) and S. pennellii. We found that the leaves of S. pennellii, a wild desert tomato relative, produces significantly more iso-alkanes than cv M82, a domesticated tomato cultivar adapted to water-replete conditions; we introduce a methylation index to summarize the ratio of branched (iso- and anteiso-) to total alkanes. Between S. pennellii and cv M82, the iso-alkanes were found to be enriched in 13C by 1.2-1.4%o over n-alkanes. By modeling our results from the ILs, we report the broad-sense heritability values (H2) of leaf wax traits to describe the degree to which genetic variation contributes to variation of these traits. Individual carbon isotope values of alkanes are of low heritability (H2 = 0.13-0.19), suggesting that {delta}13C of leaf waxes from this study are strongly influenced by environmental variance, which supports the interpretation that variation in the 5 C of wax compounds recorded in sediments reflects paleohydrological changes. Average chain length (ACL) values of n-alkanes are of intermediate heritability (H2 = 0.30), suggesting that ACL values are strongly influenced by genetic cues.

plant biology↗