Biology subjects

Johnson, A. A.

Publications and source records attributed to Johnson, A. A..

5 recordsLinked to original sources

bioRxiv2026

Whole-blood DNA-methylation patterns during portable-sauna use in firefighters: an exploratory, single-arm pilot study

Research in model organisms has consistently shown that mild, non ethal heat stress can prolong lifespan. Although causal data are lacking in more complex animals, human observational research has linked sauna bathing to cardiovascular protection and improved age related outcomes. To examine whether sauna use may influence aging related biology, we retrospectively analyzed longitudinal whole-blood methylomic data from 18 firefighters who used a portable sauna. A separately processed cohort of 36 matched adults provided descriptive context; firefighters showed higher DNA methylation estimated maximal oxygen uptake (DNAmVO2 max), lower AdaptAge, and higher DamAge. After 8 to 18 weeks, eight predictors met a within family Benjamini Hochberg false discovery rate (FDR) threshold of <0.05 underage/sex-adjusted epigenetic age acceleration: PCDNAmTL, DepressionBarbu, SystemsAge Blood, SystemsAge Lung, DNAmPulsePressure, DNAmHDL, DNAmCystatinC, and DNAmDHEAS. DNAmDHEAS increased, whereas the other predictors changed in directions consistent with short term findings for high intensity interval training, another hormetic stressor. None met the within family FDR threshold after adjustment for 12 cell leukocyte composition, although effect estimates were not uniformly eliminated. At individual cytosine-phosphate-guanine (CpG) sites, BACON empirical null calibration retained 126 acute and 329 long-term candidates at P<0.0001; none was FDR-significant. DMRcate identified five acute and 140 long-term differentially methylated regions using a harmonic mean of individual CpG FDR values <0.05. Long-term gometh analysis also identified ATP binding cassette (ABC) transporter enrichment (FDR=0.026). These exploratory findings suggest that portable-sauna use may influence the blood methylome within 8 to 18 weeks while underscoring the importance of leukocyte-composition and technical sensitivity analyses.

physiology↗

bioRxiv2026

Genetic code expansion enables plant-directed control of bacterial activity

Programmable control of microbial gene expression by plant hosts could enable a new generation of precision agricultural biotechnology. Here, using O-methyl-L-tyrosine (OMY) as a model compound, we establish non-canonical amino acids (ncAAs) as a tool for plant-based control of associated microbial activity. We use genetic code expansion to engineer OMY-dependent control of protein synthesis in the soil bacterium Bacillus subtilis. Then, we engineer agronomically diverse plants, including Arabidopsis, tomato and poplar, to biosynthesize OMY. We show that plant-derived OMY can stimulate gene expression in both model and wild soil bacteria while also demonstrating that inducible and tissue-specific expression of a single biosynthetic enzyme by the plant enables on-demand control over microbial activity. This work establishes ncAAs as a tool for programming plant-microbe partnerships.

synthetic biology↗

bioRxiv2024

A circadian transcriptional sub-network and EARLY FLOWERING 3 control timing of senescence and grain nutrition in bread wheat

Circadian clocks control daily and seasonal timing of physiology and development. Because of their influence on photoperiodic flowering, variants in circadian clock genes have been selected for phenology during domestication of cereal crops. To explore the potential impact of this genetic variation on circadian-regulated traits, we investigated the relationship of the circadian clock and leaf senescence in hexaploid bread wheat. Phenotyping of a collection of elite wheat cultivars identified significant variation in circadian rhythms which was associated with timing of senescence and nutrient mobilisation efficiency. RNA sequencing revealed substantial reorganisation of the circadian-regulated transcriptome during senescence and a transcriptional sub-network representing a link between the circadian oscillator and regulators of leaf senescence. We used genotypes of multiple circadian clock genes to assign cultivars to chronotypes, which could be used to predict circadian-regulated phenotypes. This identified a deletion variant of EARLY FLOWERING 3-D1 (ELF3-D1) attributed to a phenology locus, Earliness per se (Eps-D1), and we used near-isogenic lines (NILs) to show that it affects timing of senescence and grain protein content (GPC). Thus, there are potential consequences of circadian clock genes selected for phenology on other valuable crop traits.

plant biology↗

bioRxiv2023

Inhibition of hERG K channels by verapamil at physiological temperature: Implications for the CiPA Initiative

The Comprehensive in vitro Proarrhythmia Assay (CiPA) initiative reassesses using the inhibition of hERG channels by drugs as the major determinant for assessment of a drugs potential to cause Torsades de Pointes (TdP) cardiac arrhythmias. Here we report on one phase of CiPA: independent determination of hERG inhibitory properties in order to test the reproducibility of data gathered in different labs and the practicality of using the CiPA-defined recording conditions. We measured inhibition of hERG1a potassium channels stably expressed in HEK293 cells using manual whole-cell patch-clamp electrophysiology recordings at the physiological temperature of 37{degrees}C by verapamil, a known hERG inhibitor. We report that the IC50 for inhibition (180.4nM) and the Hill coefficient (1.4) for verapamil measured in an academic lab were similar to the IC50 (204nM) and Hill coefficient (0.9) measured at the Food and Drug Administration labs, indicating low variability in measurements between labs. We report that the CiPA step voltage protocol, a series of voltage steps characterized by 10 second duration depolarizing pulses at 37{degrees}C, resulted in a very low (5%) experimental success rate per cell in our hands. To circumvent the low success rate, we shortened the duration of the depolarizing pulse to 3 seconds (from 10 seconds) and shortened the duration of interpulse intervals, which is more consistent with the duration of voltage pulses used in biophysical studies of hERG, such that the entire revised protocol was shortened from over 30 minutes to approximately 10 minutes in duration. Using the revised protocol, we found an IC50 of inhibition by verapamil of 210.5 nM and Hill coefficient of 1.2. These values were similar to those generated using the original, longer CiPA step protocol. Furthermore, our success rate using the shortened protocol rose to 25%, an increase of 5-fold over the initial protocol. In summary, we captured key pharmacological data for subsequent analysis in CiPA using a revised, shorter protocol with an enhanced success rate and an overall enhanced feasibility. We propose the shorter protocol is more pragmatic for generation of hERG channel drug inhibition data for CiPA and other regulatory sciences.

pharmacology and toxicology↗

bioRxiv2022

A two-gene strategy increases the iron and zinc concentration of wheat flour and improves mineral bioaccesibility for human nutrition.

Dietary deficiencies of iron and zinc cause human malnutrition globally, which can be mitigated by biofortified staple crops. Conventional breeding approaches to increase grain mineral concentrations in wheat (Triticum aestivum L.) have had only limited success so far due to relatively low genetic variation. Here we demonstrate that a transgenic approach combining endosperm-specific expression of the wheat vacuolar iron transporter gene TaVIT2-D with constitutive expression of the rice nicotianamine synthase gene OsNAS2 has the potential to dramatically improve mineral micronutrient intake from wheat products. In two distinct bread wheat cultivars, we show that the VIT-NAS construct led to a two-fold increase in zinc to [~]50 {micro}g g-1 in wholemeal flour and a two-fold increase in both zinc and iron in hand-milled white flour. In highly pure, roller-milled white flour, the concentration of iron was enhanced three-fold to [~]25 {micro}g g-1. A greater than three-fold increase in the level of the natural plant metal chelator nicotianamine in the grain of VIT-NAS lines was associated with improved iron and zinc bioaccessibility in white flour. The growth of VIT-NAS plants in the greenhouse was indistinguishable from untransformed controls. We conclude that the effects of each gene cassette are additive in altering the total concentration and distribution of iron and zinc in wheat grains. This demonstrates the potential of a transgenic approach to enhance the nutritional quality of wheat well beyond what is possible by breeding approaches in order to alleviate dietary mineral deficiencies.

plant biology↗