Biology subjects

Atkinson, E.

Publications and source records attributed to Atkinson, E..

7 recordsLinked to original sources

bioRxiv2026

Rapid assessment of nitrification inhibitor efficacy, competitiveness, and specificity using microrespirometry

Nitrification inhibitors are applied to reduce nitrogen losses and greenhouse gas emissions from fertilized agricultural ecosystems. However, their characterization is typically focused on determining effective inhibitor concentrations from growth or substrate conversion assays that are time-intensive and provide limited mechanistic resolution. Here, we present a microrespirometry (MR)-based workflow for rapid mechanistic characterization of nitrification inhibitors using oxygen consumption as a real-time readout for metabolic activity. The workflow enables the simultaneous assessment of inhibitor efficacy, competitiveness, and enzyme specificity within a single experimental setup, as sequential substrate and inhibitor additions enable direct discrimination between competitive and non-competitive inhibition and between ammonia monooxygenase-specific and broader respiratory inhibition. As a proof of concept, we evaluated three known nitrification inhibitors phenylacetylene (PA), nitrapyrin (NP), and dicyandiamide (DCD) using the ammonia-oxidizing bacteria Nitrosomonas europaea and Nitrosospira multiformis, the complete ammonia oxidizer Nitrospira inopinata, and the nitrite oxidizer Nitrospira moscoviensis. We also compared the results from the MR-based inhibition workflow with those from a conventional growth-based approach and observed a poor correlation between results for inhibitors that are not fully enzyme specific. In conclusion, this work establishes MR as a rapid and versatile platform for the mechanistic screening of novel potential nitrification inhibitors. MR assays reproduce known inhibitory responses while substantially reducing experimental time and increasing mechanistic resolution compared to other assays types. Additionally, we provide the first pure-culture characterization of PA, NP, and DCD efficacy and inhibition mechanisms in a complete ammonia oxidizer, N. inopinata.

microbiology↗

bioRxiv2025

Pupation substrate and prepupal handling affect eclosion rate, timing, and adult morphology in black soldier flies (Hermetia illucens; Diptera: Stratiomyidae)

On farms, the conditions experienced by black soldier fly (BSF) prepupae may impact their development and survival, altering production goals by changing the fitness of breeding adults. Few studies have addressed the impact of environmental variables (such as substrate type or moisture content), or stressors like handling, on the development and survival of BSF as they transition from prepupae through adulthood. This study examined the effects of pupation substrate (corn cob grits, potting soil, vermiculite, wood chips, and frass), moisture content (20%, 60%, and 100%), and handling during the prepupal period (daily handling, no handling) on eclosion rate and timing, morphology (mass, head width, thorax length), and abdominal window fullness of adult BSF. Handling delayed adult emergence by over three days, reduced eclosion rates by 30.6%, reduced head width and wet mass in adult males, and reduced window fullness and head width in adult females. Frass resulted in the lowest eclosion rate (72.1 {+/-} 2.4%) while corn cob grits (82.2 {+/-} 2.3%) and wood chips (81.5 {+/-} 2.2%) had the highest. Wood chips also resulted in the highest wet and dry mass, head width, and thorax length for adult males and females. Wood chips may be the best pupation substrate for BSF as it enhances body size and has a good eclosion rate. Significant prepupal handling delays adult emergence, reduces eclosion/survival rates, and reduces adult body size; however, more research is necessary to determine if the less chronic handling regimes that are likely present on farms produce similar effects.

zoology↗

bioRxiv2025

Corticospinal, reticulospinal, and motoneuronal contributions to fatigability during a sustained contraction of the elbow flexors

Synaptic input to the motoneuron pool is altered during fatiguing muscle contractions. In humans, the corticospinal tract is often studied, with equivocal findings regarding its role in the reduction of force. To date, the involvement of the reticulospinal tract during states of fatigue has not been explored. Fourteen participants (28{+/-}6 years, nine males) visited the laboratory twice, first for a familiarisation, then an experimental trial. Participants completed a 5-min sustained elbow flexor contraction at an intensity eliciting 40% of the EMG recorded during a maximal isometric voluntary contraction (MVC). Before, during, and after the contraction, transcranial magnetic stimulation and electrical cervicomedullary stimulation were used to elicit motor evoked potentials (MEPs) and cervicomedullary evoked potentials during the silent period (SP-CMEPs) respectively, with CMEPs also being evoked in combination with a startling acoustic sound (CMEPcon). Electrical stimulation of the brachial plexus was used to evoke maximal compound action potentials of the elbow flexors (Mmax). The 5-min contraction induced a 53% loss of force (p<0.001), with no change in background EMG ([~]4% Mmax, p=0.293). Neither MEP amplitude (p=0.246) nor CMEPcon ratio (p=0.489) were altered during the contraction. Whereas CMEP and SP-CMEP amplitudes were reduced by [~]20 and 50%, respectively (p<0.001) and remained depressed post-task. The results suggest that neither corticospinal nor reticulospinal tract excitability was altered during a 5-min constant-EMG task at 40% maximal EMG. Instead, the aetiology of the neural contribution to fatigability appeared to be primarily related to the loss of motoneuron excitability.

neuroscience↗

bioRxiv2023

In vitro and in vivo effects of zoledronate on senescence and senescence-associated secretory phenotype markers

In addition to reducing fracture risk, zoledronate has been found in some studies to decrease mortality in humans and extend lifespan and healthspan in animals. Because senescent cells accumulate with aging and contribute to multiple co-morbidities, the non-skeletal actions of zoledronate could be due to senolytic (killing of senescent cells) or senomorphic (inhibition of the secretion of the senescence-associated secretory phenotype [SASP]) actions. To test this, we first performed in vitro senescence assays using human lung fibroblasts and DNA repair-deficient mouse embryonic fibroblasts, which demonstrated that zoledronate killed senescent cells with minimal effects on non-senescent cells. Next, in aged mice treated with zoledronate or vehicle for 8 weeks, zoledronate significantly reduced circulating SASP factors, including CCL7, IL-1{beta}, TNFRSF1A, and TGF{beta}1 and improved grip strength. Analysis of publicly available RNAseq data from CD115+ (CSF1R/c-fms+) pre-osteoclastic cells isolated from mice treated with zoledronate demonstrated a significant downregulation of senescence/SASP genes (SenMayo). To establish that these cells are potential senolytic/senomorphic targets of zoledronate, we used single cell proteomic analysis (cytometry by time of flight [CyTOF]) and demonstrated that zoledronate significantly reduced the number of pre-osteoclastic (CD115+/CD3e-/Ly6G-/CD45R-) cells and decreased protein levels of p16, p21, and SASP markers in these cells without affecting other immune cell populations. Collectively, our findings demonstrate that zoledronate has senolytic effects in vitro and modulates senescence/SASP biomarkers in vivo. These data point to the need for additional studies testing zoledronate and/or other bisphosphonate derivatives for senotherapeutic efficacy.

physiology↗

bioRxiv2021

Neural bases of risky decisions involving nicotine vapor versus monetary reward

Substantial effort has gone into neuroimaging studies of neural mechanisms underlying addiction. Human studies of smoking typically either give monetary reward during an fMRI task or else allow subjects to smoke outside the scanner, after the session. This raises a fundamental issue of construct validity, as it is unclear whether the same neural mechanisms process decisions about nicotine that process decisions about money. To address this, we developed a novel MR-compatible nicotine vaping device, such that access to nicotine vapor could be controlled and monitored. We recruited heavy smokers to perform a gambling task with nicotine and monetary reward on separate days. This allowed a direct comparison between the neural mechanisms of choosing and receiving immediate drug vs. monetary reward. We found substantial differences in the neural mechanisms that underlie risky choices about money vs. drug reward, including a reversal of the well-known error effects in the medial prefrontal cortex.

neuroscience↗

bioRxiv2020

The impact of non-additive genetic associations on age-related complex diseases.

Genome-wide association studies (GWAS) are not fully comprehensive as current strategies typically test only the additive model, exclude the X chromosome, and use only one reference panel for genotype imputation. We implemented an extensive GWAS strategy, GUIDANCE, which improves genotype imputation by using multiple reference panels, includes the analysis of the X chromosome and non-additive models to test for association. We applied this methodology to 62,281 subjects across 22 age-related diseases and identified 94 genome-wide associated loci, including 26 previously unreported. We observed that 27.6% of the 94 loci would be missed if we only used standard imputation strategies and only tested the additive model. Among the new findings, we identified three novel low-frequency recessive variants with odds ratios larger than 4, which would need at least a three-fold larger sample size to be detected under the additive model. This study highlights the benefits of applying innovative strategies to better uncover the genetic architecture of complex diseases.

genomics↗

bioRxiv2020

Targeting the Src pathway enhances the efficacy of selective FGFR inhibitors in cancers with FGFR3 alterations

Selective FGFR inhibitors such as infigratinib (BGJ398) and erdafitinib (JNJ-42756493) have been evaluated in clinical trials for cancers with FGFR3 molecular alterations, particularly in urothelial carcinoma patients. However, a substantial proportion of these patients (up to 50%) display intrinsic resistance to these drugs and receive minimal clinical benefit. There is thus an unmet need for alternative therapeutic strategies to overcome primary resistance to selective FGFR inhibitors. In this study, we demonstrate that cells expressing cancer-associated activating FGFR3 mutants and the FGFR3-TACC3 fusion showed primary resistance to infigratinib in long-term colony formation assays in both NIH-3T3 and urothelial carcinoma models. We find that expression of these FGFR3 molecular alterations resulted in elevated constitutive Src activation compared to wildtype FGFR3 and that cells co-opted this pathway as a means to achieve intrinsic resistance to infigratinib. Targeting the Src pathway with low doses of the kinase inhibitor dasatinib synergistically sensitized multiple urothelial carcinoma lines harbouring endogenous FGFR3 alterations to infigratinib. Our preclinical data provides evidence that supports the use of dasatinib in combination with selective FGFR inhibitors as a means to overcome intrinsic drug resistance in the salvage therapy setting in cancer patients with FGFR3 molecular alterations.

cancer biology↗