Biology subjects

Logan, A.

Publications and source records attributed to Logan, A..

4 recordsLinked to original sources

bioRxiv2026

Formate-driven isoprene reduction enables energetic independence in Pelotomaculum schinkii: Evidence from metatranscriptomic and functional analyses

Isoprene, a volatile hydrocarbon emitted in vast quantities by terrestrial vegetation, can serve as a terminal electron acceptor in anoxic environments. Here, we investigated the molecular and physiological basis of isoprene reduction in an anaerobic enrichment culture highly enriched in Pelotomaculum. Substrate-exclusion assays revealed that formate is indispensable for isoprene reduction: cultures lacking formate showed no isoprene reduction, whereas formate alone sustained both reduction activity and the highest enrichment of Pelotomaculum. Metatranscriptomic analyses confirmed that Pelotomaculum schinkii was the most transcriptionally active species under isoprene-amended conditions, whereas Sedimentibacter saalensis was most enriched in unamended controls. Isoprene-treated cultures exhibited strong upregulation of [NiFe]-hydrogenase maturation factors (hypA/hybF, hypB), energy-conserving complexes (ATP synthase, H /Na - translocating pyrophosphatases), and transport systems (FeoB, ModBC), consistent with a formate-driven respiratory pathway. In contrast, genes for oxidative stress and metal detoxification were enriched in controls, suggesting physiological stress in the absence of isoprene. Thermodynamic calculations further supported this mechanism, showing that formate oxidation coupled to isoprene reduction is highly favorable ({Delta}G{degrees}' {approx} -135 kJ/mol), with an energy yield far exceeding that of formate-driven hydrogen production. Together, these findings support two mechanistic models: (i) direct isoprene reduction by group 4b [NiFe]-hydrogenase or (ii) indirect reduction via hydrogen transfer to an isrA-like oxidoreductase, analogous to Acetobacterium wieringae ISORED-2. Our results demonstrate that P. schinkii, a metabolically versatile bacterium, couples formate oxidation to isoprene respiration, indicating that isoprene can serve as an alternative electron sink. This allows P. schinkii to escape obligate syntropy with methanogens and alters microbial activity and energy conservation in anoxic ecosystems.

microbiology↗

bioRxiv2025

Measurement Quality Metrics to Improve Absolute Microbial Cell Counting

Total and viable microbial cell counts are increasingly important for applications including live biotherapeutic products, food safety, and probiotics. In microbiology, cells are quantified using methods such as colony forming unit (CFU), flow cytometry, and polymerase chain reaction (PCR), but different methods measure different aspects of the cells (measurands), and results may not be directly comparable across methods. In the absence of a ground-truth reference material for cell count, one cannot quantify the accuracy of any cell counting method, which limits method performance assessments and comparisons. Herein, a modified analysis of cell counting methods based on the ISO 20391-2:2019 standard was developed and demonstrated for microbial cell samples diluted over a log-scale range of concentrations. Escherichia coli samples ranging in concentration from approximately 5 x 105 cells/mL to 2 x 107 cells/mL were quantified using CFU, Coulter principle, fluorescence flow cytometry, and impedance flow cytometry. Quality metrics modified from the ISO standard were calculated for each method and shown to be repeatable across replicate experiments. The quality metrics illustrate large differences in proportionality and variability across methods, with total cell counts in good agreement and viable cell count having more variability. As the ISO standard is meant to guide fit-for-purpose method selection, interpretation of the results and quality metrics can drive method choice and optimization. The framework introduced here will help researchers select fit-for-purpose counting methods for quantification of microbial total and viable cells across a range of applications.

microbiology↗

bioRxiv2022

A clinical stage LMW-DS drug inhibits cell infection by coronaviruses and modulates reactive cytokine release from microglia

Most coronaviruses infect animals including bats, birds and mammals, which act as hosts and reservoirs for the viruses, but the viruses can sometimes move host species and infect humans. Coronoviruses were first identified as human pathogens in the 1960s and now there are seven types known to infect humans. Whilst four of these types cause mild-to-moderate respiratory disease, the other three may cause more severe and possibly even fatal disease in vulnerable individuals particularly, with the most recent SARS-CoV-2 pandemic being associated with severe acute respiratory syndrome (SARS) in many infected people. The aim of the present study was to evaluate the potential of a unique low molecular weight dextran sulphate (LMW-DS) clinical stage drug, ILB(R), to inhibit infection of human cells by the NL63 coronavirus assessed by immunofluorescence of viral particles, and also to see if the drug directly blocked the interaction of the SARS-CoV-2 viral spike protein with the ACE2 receptor. Furthermore, we evaluated if ILB(R) could modulate the downstream consequences of viral infection including the reactive cytokine release from human microglia induced by various SARS-CoV-2 variant spike proteins. We demonstrated that ILB(R) blocked ACE2:spike protein interaction and inhibited coronaviral infection. ILB(R) also attenuated the omicron-induced release of pro-inflammatory cytokines, including TNF, from human microglia, indicating control of post-viral neuroinflammation. In conclusion, given the safety profile of ILB(R) established in a number of Phase I and Phase II clinical trials, these results highlight the potential of ILB(R) to treat patients infected with coronaviruses to both limit infectivity and attenuate the progression to severe disease. There is now an opportunity to translate these findings quickly by the clinical investigation of drug efficacy.

immunology↗

bioRxiv2022

A clinical stage LMW-DS drug inhibits infection of human cells by Dengue, Zika and Yellow Fever viruses

The flavivirus family are responsible for the most abundant arboviral diseases of humans in terms of geographical distribution, morbidity and mortality; at least 2.5 billion people are at risk with, for example, an estimated 100-400 million Dengue infections a year. However, for infections by Dengue, Zika or Yellow Fever virus there are no effective anti-infective drug treatments nor for Dengue or Zika virus a safe effective vaccine and prevention at present focusses on vector (mosquito) control. Whilst symptoms from Dengue, Zika and Yellow Fever virus infection may be mild for some, they are very serious and life threatening for others. For instance, severe Dengue is a leading cause of hospitalisation and death among children and adults in Asian and Latin American countries. Likewise, Zika infection can have catastrophic consequences for pregnant women following the passing of the virus to their foetus with arising miscarriage or birth defects including microcephaly that can be fatal. The aim of the present study was to evaluate the potential of a unique low molecular weight dextran sulphate (LMW-DS) clinical stage drug, ILB(R), to inhibit infection of human cells by four serotypes of Dengue virus (DENV1-4), two strains of Zika virus (African and Asian) and Yellow Fever virus (vaccine strain YF17D) assessed by immunofluorescence of viral particles. ILB(R) potently inhibited infection by all the strains of Dengue, Zika and Yellow Fever virus in a concentration-dependent manner with IC50 for ILB(R) ranging from 31 to 343 g/ml. In conclusion, given the safety profile of ILB(R) established in a number of Phase I and Phase II clinical trials, these results highlight the potential of ILB(R) to treat patients infected with Dengue, Zika or Yellow Fever virus with the opportunity to translate the findings quickly by clinical investigation.

immunology↗