Biology subjects

Lewis, I.

Publications and source records attributed to Lewis, I..

9 recordsLinked to original sources

bioRxiv2026

No Effect of Exercise Timing on Daily Glycaemia Despite Shifts in Acute Glucose Dynamics in Participants with Normal Glucose Tolerance: A Randomised Crossover Trial

Exercise is a well-established modulator of glucose regulation, but whether the time of day it is performed matters for healthy, free-living adults remains unresolved. In a randomised crossover trial, 29 healthy adults completed a single 30-minute bout of moderate-intensity exercise in the morning (07:00-10:00) and in the evening (16:00-19:00), with continuous glucose monitoring and wrist-worn activity tracking used to capture responses over an 8-day free-living protocol. Evening exercise produced a significantly greater acute reduction in blood glucose (P < 0.001) compared to morning exercise, but this did not translate into consistent differences in overall daily mean glycaemic exposure, whether measured over the calendar day or over a window aligned with exercise onset. Evening exercise was linked to greater within-day glycaemic variability than morning exercise, with the clearest evidence coming from the circadian-aligned analysis (day x timing interaction, SD: P = 0.00939; CV: P = 0.00766). Appetite rose after exercise in both conditions, with no difference by time of day. Taken together, these results show that exercise timing does not change how much glucose exposure a healthy adult accumulates over a day, but it does change the shape of the glucose response around the exercise bout itself, a distinction only visible when glucose is examined at a finer temporal resolution than daily averages allow.

physiology↗

bioRxiv2026

Multi omics reveals mesodermal fate bias and enables predictive cell state control in human pluripotent stem cell biomanufacturing

Human induced pluripotent stem cells can retain conventional markers of pluripotency while acquiring environmentally dependent molecular states that may influence their developmental competence. Yet, how biomanufacturing conditions reorganize the interconnected networks governing cell state remains poorly characterized. Here, we first examined compensation of hiPSCs to static aggregation and dynamic agitation by proteomics. We then examined hiPSCs during single-passage culture in stirred-suspension bioprocesses under varying oxygen and agitation conditions. Intracellular metabolomic and transcriptomic profiling revealed distinct responses across culture configuration, hydrodynamic exposure, and oxygenation. Transition into dynamic culture broadly remodeled mitochondrial organization, carbon allocation, mechanotransduction, proteostasis, and developmental regulation. Increasing agitation produced a persistent response involving cellular architecture, growth-factor signaling, genome maintenance, and Epiblast- and lineage-aligned programs, whereas oxygenation elicited a smaller and more transient metabolic and transcriptional response. Through comparison with a human gastrulation reference, we show that these adaptations intersect with natural developmental programs without reproducing coherent epiblast state or lineage commitment. These findings demonstrate that bioprocess conditions can preserve core pluripotent identity while remodeling broader molecular states associated with developmental responsiveness, providing perspective on evaluating and optimizing hiPSC quality in biomanufacturing beyond restricted marker panels.

bioengineering↗

bioRxiv2026

T6SS mutants exploit itaconate to support infection of phagocytes

Pseudomonas aeruginosa is a major cause of persistent pneumonias that are not readily cleared by seemingly appropriate antimicrobial therapy. We identified a reservoir of P. aeruginosa variants lacking expression of the H3-T6SS in patients with chronic but not acute pneumonia. A PAO1 {Delta}H3-T6 mutant caused increased infection in the murine lung as compared to the wild-type strain. The {Delta}H3 mutants exhibited increased transcription of genes involved in phagocytic uptake and respiration under conditions found in the phagolysosome, namely low O2, low pH and abundant itaconate. We confirmed increased intraphagocytic residence of the {Delta}H3 mutants and colocalization with LAMP1 within the phagolysosome of both bone marrow derived macrophages in vitro and in alveolar macrophages harvested directly from infected lungs. Persistence within macrophages required itaconate which preserved the viability of infected macrophages and boosted bacterial bioenergetics to optimize consumption of available carbon sources. Our findings demonstrate that selection for loss of H3-T6SS loss of function mutations promotes the metabolic versatility that enables P. aeruginosa to cause intractable pulmonary infection.

immunology↗

bioRxiv2025

Life-history evolution under artificial selection in a clonal plant

The response of natural populations to selection and the role of genetic correlations in constraining or facilitating evolutionary change is fundamental to adaptation. We use artificial selection to investigate the evolutionary response of clonal reproduction in the common monkeyflower (Mimulus guttatus), a species with extensive life history variation. We first characterize the standing genetic variation in a single perennial population, and then conduct four generations of divergent artificial selection on stolon number--the mechanism of clonal reproduction in this species. To start, stolon number had moderate heritability (H{superscript 2}=0.25) and was negatively genetically correlated with reproductive traits. Artificial selection produced a clear but asymmetrical response. High selection lines made significantly more stolons, while low lines diverged less from controls. Analyses of G matrices revealed that selection not only changed trait means but also genetic correlations, with high lines diverging more in multivariate genetic architecture. Our results demonstrate that single populations harbor sufficient genetic variation to respond rapidly to selection on clonality, and the response is shaped by existing patterns of genetic covariation. The capacity for rapid evolution of clonal traits is particularly relevant as climate change alters selection and shifts the relative advantages of sexual versus clonal life-history strategies.

evolutionary biology↗

bioRxiv2025

Sequestration of the phagocyte metabolite itaconate by P. aeruginosa RpoN promotes successful pulmonary infection

AbstractThe phagocyte immunometabolite itaconate, normally toxic to bacteria, functions as a signal to stimulate the adaptation of the pulmonary pathogen Pseudomonas aeruginosa to the lung. Itaconate is actively transported into P. aeruginosa where it induces {sigma}54 rpoN expression and co-valently binds cysteine residues on RpoN. RpoN not only functions as a sink to limit itaconate toxicity but S- itaconated RpoN promotes increased utilization of the Entner Doudoroff pathway, optimizing bacterial metabolism in the setting of inflammation. S-itaconation of RpoN directs a global metabolic response that fuels pulmonary infection.

microbiology↗

bioRxiv2023

Multiple domains of the integral KREPA3 protein are critical for the structure and precise functions of RNA Editing Catalytic Complexes in Trypanosoma brucei

The gRNA directed U-insertion and deletion editing of mitochondrial mRNAs that is essential in different life cycle stages for the protozoan parasite Trypanosoma brucei is performed by three similar multi-protein catalytic complexes (CCs) that contain the requisite enzymes. These CCs also contain a common set of eight proteins that have no apparent direct catalytic function, including six that have an OB-fold domain. We show here that one of these OB-fold proteins, KREPA3 (A3), has structural homology to other editing proteins, is essential for editing and is multifunctional. We investigated A3 function by analyzing the effects of single amino acid loss of function mutations most of which were identified by screening bloodstream form (BF) parasites for loss of growth following random mutagenesis. Mutations in the ZFs, an intrinsically disordered region (IDR) and several within or near the C-terminal OB-fold domain variably impacted CC structural integrity and editing. Some mutations resulted in almost complete loss of CCs and its proteins and editing whereas others retained CCs but had aberrant editing. All but a mutation which is near the OB-fold affected growth and editing in BF but not procyclic form (PF) parasites. These data indicate that multiple positions within A3 have essential functions that contribute to the structural integrity of CCs, the precision of editing and the developmental differences in editing between BF and PF stages.

molecular biology↗

bioRxiv2023

mt-LAF3 is a pseudouridine synthase ortholog required for mitochondrial rRNA and mRNA gene expression in Trypanosoma brucei

Trypanosoma brucei and related kinetoplastid parasites possess unique RNA processing pathways, including in their mitochondria, that regulate metabolism and development. Altering RNA composition or conformation through nucleotide modifications is one such pathway, and modifications including pseudouridine regulate RNA fate and function in many organisms. We surveyed pseudouridine synthase (PUS) orthologs in Trypanosomatids, with a particular interest in mitochondrial enzymes due to their potential importance for mitochondrial function and metabolism. T. brucei mt-LAF3 is an ortholog of human and yeast mitochondrial PUS enzymes, and a mitoribosome assembly factor, but structural studies differ in their conclusion as to whether it has PUS catalytic activity. Here, we generated T. brucei cells that are conditionally null for mt-LAF3 and showed that mt-LAF3 loss is lethal and disrupts mitochondrial membrane potential ({Delta}{Psi}m). Addition of a mutant gamma-ATP synthase allele to the conditionally null cells permitted {Delta}{Psi}m maintenance and cell survival, allowing us to assess primary effects on mitochondrial RNAs. As expected, these studies showed that loss of mt-LAF3 dramatically decreases levels of mitochondrial 12S and 9S rRNAs. Notably, we also observed decreases in mitochondrial mRNA levels, including differential effects on edited vs. pre-edited mRNAs, indicating that mt-LAF3 is required for mitochondrial rRNA and mRNA processing, including of edited transcripts. To assess the importance of PUS catalytic activity in mt-LAF3 we mutated a conserved aspartate that is necessary for catalysis in other PUS enzymes and showed it is not essential for cell growth, or maintenance of {Delta}{Psi}m and mitochondrial RNA levels. Together, these results indicate that mt-LAF3 is required for normal expression of mitochondrial mRNAs in addition to rRNAs, but that PUS catalytic activity is not required for these functions. Instead, our work, combined with previous structural studies, suggests that T. brucei mt-LAF3 acts as a mitochondrial RNA-stabilizing scaffold.

microbiology↗

bioRxiv2022

The immune response to lumpy skin disease virus in cattle is influenced by inoculation route

Lumpy skin disease virus (LSDV) causes severe disease in cattle and water buffalo and is transmitted by hematophagous arthropod vectors. Detailed information of the adaptive and innate immune response to LSDV is limited, hampering the development of tools to control the disease. This study provides an in-depth analysis of the immune responses of calves experimentally inoculated with LSDV via either needle-inoculation or arthropod-inoculation using virus-positive Stomoxys calcitrans and Aedes aegypti vectors. Seven out of seventeen needle-inoculated calves (41%) developed clinical disease characterised by multifocal necrotic cutaneous nodules. In comparison 8/10 (80%) of the arthropod-inoculated calves developed clinical disease. A variable LSDV-specific IFN-{gamma} immune response was detected in the needle-inoculated calves from 5 days post inoculation (dpi) onwards, with no difference between clinical calves (developed cutaneous lesions) and nonclinical calves (did not develop cutaneous lesions). In contrast a robust and uniform cell-mediated immune response was detected in all eight clinical arthropod-inoculated calves, with little response detected in the two nonclinical arthropod-inoculated calves. Neutralising antibodies against LSDV were detected in all inoculated cattle from 5-7 dpi. Comparison of the production of anti-LSDV IgM and IgG antibodies revealed no difference between clinical and nonclinical needle-inoculated calves, however a strong IgM response was evident in the nonclinical arthropod-inoculated calves but absent in the clinical arthropod-inoculated calves. This suggests that early IgM production is a correlate of protection in LSD. This study presents the first evidence of differences in the immune response between clinical and nonclinical cattle and highlights the importance of using a relevant transmission model when studying LSD.

immunology↗

bioRxiv2020

Immunotherapy efficacy in colorectal cancer is dependent on activation of a microbial-metabolite-immune circuit

Cancer is a leading cause of death globally. Checkpoint blockade therapies offer a promising treatment for many cancers, but have been ineffective for colorectal cancers. Previous studies have shown a dependency of immunotherapies on the microbiota. Consequently, we hypothesized that specific gut bacteria promote immunotherapy for colorectal cancer. We identify three commensal bacteria and a microbial metabolite, inosine, that enhance the efficacy of immune checkpoint blockade therapy in colorectal cancer. We show that inosine interacts with the adenosine A2A receptor on T cells resulting in intestinal Th1 cell differentiation. Decreased gut barrier function induced by immunotherapy increased the translocation of bacterial metabolites and promoted cancer protective Th1 cell activation. This microbial-metabolite-immune circuit provides a mechanism for a new class of bacteria-enhanced checkpoint blockade therapies. The efficacy of this mechanism differs among colorectal cancer subtypes and highlights the strengths as well as potential limitations of this novel bacterial co-therapy for cancer.

cancer biology↗