Biology subjects

Lewis, M.

Publications and source records attributed to Lewis, M..

At least 19 recordsLinked to original sources

bioRxiv2026

Network and behavioral signatures of postpartum behavioral deficits improve with a neurosteroid-based treatment

Postpartum depression (PPD) impacts nearly 20% of mothers and a much larger percentage (up to 75%) suffer from postpartum blues. Despite this high incidence, we still have an incomplete understanding of the underlying neurobiology of PPD. Deficits in neurosteroid signaling has been implicated in the vulnerability to postpartum behavioral deficits and mice with reduced expression of {delta} subunit-containing GABAA receptors (GABAARs) (Gabrd -/- or Gabrd +/-), the predominant site of action for 5-reduced neurosteroids, exhibit behavioral deficits restricted to the postpartum period. Allopregnanolone and allopregnanolone analogs (SGE-516) can improve postpartum behavioral outcomes and their ability to modulate oscillations in the basolateral amygdala (BLA) involved in emotional processing has been proposed to contribute to their antidepressant effects. Here we demonstrate that the behavioral differences in postpartum wild type, Gabrd+/-, and SGE-516-treated Gabrd+/- dams is largely driven by theta oscillations in the BLA. Previous studies have linked theta oscillations in the BLA to altered behavioral responding in response to stress or threat. Interestingly, here we demonstrate that Gabrd+/- dams exhibit a failure to properly respond to their own pup calls, with reduced theta oscillations that correlates with deficits in maternal approach behavior both of which are restored with SGE-516 treatment. Further, unbiased MoSeq analysis identified altered behavioral syllable expression in Gabrd+/- dams in response to their pup calls compared to wild type dams that are restored with SGE-516 treatment. These findings demonstrate network and behavioral signatures of postpartum behavioral deficits and characterize the effects associated with neurosteroid-based treatment response.

neuroscience↗

bioRxiv2026

Widespread detection of Polyethylene glycol reveals chronic human exposure through pharmaceutical drugs

Polyethylene glycol (PEG) is a synthetic polymer ubiquitous in pharmaceuticals, personal care products, food additives, and industrial manufacturing. Despite its widespread use and potential importance as an exposure chemical, the prevalence of PEG exposure and its excretion in human populations remain largely uncharacterized. Moreover, PEG detected in human biofluids is frequently assumed to arise from analytical contamination during sample preparation, potentially obscuring its contribution to the human exposome and confounding metabolic phenotyping studies. Here, we show that PEG is as component of the human xenobiotic exposome and is further metabolized into PEG hydoxy acid and diacid metabolites in humans. We further find that PEG exposure is associated with alterations in microbiome composition and short-chain fatty acid metabolism, suggesting its biological impact of its exposure. We identify PEG exposure in approximately 2.3% of publicly available metabolomics data files and provide a reusable 85,484 candidate PEG and PEGylated MS/MS spectral library for future use for the metabolomic community. Together, these findings establish PEG signal in human biofluids can reflect genuine exposure, and that PEG exposure is neither metabolically inert nor biologically silent.

biochemistry↗

bioRxiv2026

Why architecture matters: Controlling gene expression through design

Inducible gene expression systems are widely used in synthetic biology and gene therapy, yet their performance depends not only on regulator chemistry but also on circuit architecture. Here, we examine how promoter organization shapes TetR-based gene regulation in mammalian cells using a panel of single-vector constructs spanning a broad range of promoter strengths. Experiments and thermodynamic models show that bidirectional circuits impose a trade-off between output and control: increasing promoter strength elevates both induced and basal expression, compressing dynamic range. Incorporating transcriptional coupling explains the parallel scaling of these states in compact divergent designs. In contrast, autogenous regulation couples repressor production to transcription, introducing negative feedback that buffers promoter strength and preserves fold induction. Finally, adding ligand-responsive aptazymes as a post-transcriptional layer further suppresses basal expression while maintaining inducibility, albeit with reduced maximal output. Together, these results identify regulatory architecture as a primary determinant of circuit performance and establish design principles for constructing more predictable gene expression systems in eukaryotic cells.

molecular biology↗

bioRxiv2026

Allosteric Constraints on Rewiring Inducible Repressors

Precise chemical control of transgene expression is central to synthetic biology, mammalian cell engineering, and gene therapy. Although tetracycline-responsive systems are widely used, converting an inducible repressor into a robust co-repressible regulator remains difficult. Systems engineered to activate DNA binding in response to ligand often exhibit elevated basal expression, weak switching, and limited dynamic range, suggesting that regulatory polarity is constrained by the underlying allosteric free-energy landscape. Here we combine thermodynamic modeling with matched mammalian reporter assays to examine the fundamental distinction between inducible and co-repressible regulation. Using a promoter-occupancy framework, we describe how ligand binding redistributes regulators between DNA-binding-competent and DNA-binding-incompetent conformations to control transcriptional output. Inducible repressors such as TetR activate transcription by reducing operator occupancy, whereas co-repressible systems must increase operator occupancy to suppress transcription, imposing fundamentally different energetic requirements. Experimental comparison of TetR-derived and PurR-derived regulators supports this thermodynamic interpretation. TetR-based systems produced strong ligand-dependent induction, whereas reverse TetR variants exhibited weaker co-repressible behavior and higher residual expression. In contrast, the natural co-repressible regulator PurR responded to hypoxanthine with ligand-stabilized DNA binding, and PurR-VP16 produced stronger ligand-dependent transcriptional activation than reverse TetR. Together, these results show that regulatory performance is determined by how efficiently ligand binding redistributes conformational states and suggest that natural co-repressible scaffolds may provide superior foundations for engineering ligand-activated transcriptional control.

biochemistry↗

bioRxiv2026

AI-enabled rhodopsin design for blue-light enhanced bacterial growth

We developed an AI-guided design pipeline that generated and validated non-natural microbial rhodopsins with spectral properties not yet known in nature. The pipeline comprised a three-stage in silico design, a genetic algorithm (GA) for sequence generation, a stacked LASSO and XGBoost machine-learning (ML) regressor for spectral prediction and fitness ranking, and a Markov-based sequence plausibility filter to enforce proton pumping like characteristics. Four candidate rhodopsins (APR1, APR2, APR6, and APR7) targeting blue light absorption were designed and AlphaFold3 structural modelling predicted retinal binding pocket architecture consistent with outward proton-pumping function. Experimental characterisation confirmed that all four variants absorbed light at [~]410 nm and significantly promoted the growth of Cupriavidus necator under blue light illumination. This study demonstrates that AI-enabled design can engineer proteins with no natural precedent, generating light-harvesting rhodopsins with novel spectral properties while preserving biological function, marking a significant advance in programmable synthetic biology.

Synthetic Biology↗

bioRxiv2026

Live triatomine bug, vector of Trypanosoma cruzi (Chagas disease), found engorged in Lisbon hotel room: A first for Portugal and for Europe

Triatomine bugs are blood feeding insects that transmit the parasite Trypanosoma cruzi, causative agent of Chagas disease. The bugs are found primarily in the Americas with a few species in Asia and Africa. Here we report the first case of a live triatomine bug in Europe, found in a Lisbon hotel room. In August, 2025, the hotel room occupants discovered a triatomine bug perched on the headboard of their bed. Upon capture, bright red blood emerged from the bug; the occupants suspected that it had bitten them during the night. The bug was identified morphologically as triatomine species Hospesneotomae protracta, which was confirmed molecularly. Hospesneotomae protracta is native to the southwestern United States where it is a competent T. cruzi vector. Trypanosoma cruzi was not detected in this specimen. Although this case likely represents an accidental importation, it illustrates the ease with which disease vectors can be unknowingly transported globally. Ergo it is crucial to document and share these findings to prevent introductions of non-native arthropods of medical importance.

ecology↗

bioRxiv2026

Orphan GPR84 facilitates uropod de-adhesion to terminate leukocyte diapedesis during inflammation

Leukocyte migration through venular walls is an essential component of effective immunity. While the key molecular players driving the initial steps of this response are known, the terminating signals remain unclear. Here, we have identified a conserved role for GPR84 family GPCRs in successful completion of the final stages of leukocyte extravasation through acutely inflamed vessels. The integration of high resolution intravital imaging with cell-specific genetics revealed that genetic deficiency of GPR84 orthologues in mice and Drosophila, results in defective detachment of transmigrating immune cells from vessel walls. Mechanistically, transcriptomics revealed GPR84-deficient neutrophils exhibit defective actin cytoskeletal regulation and cellular adhesion/de-adhesion. Consistent with this, our fly-murine pipeline shows that GPR84 supports localized and dynamic Rho activation to enable detachment of the immune cell uropod from vessel exit sites. Moreover, pharmacological blockade of GPR84 signaling dampened immune cell migration in multiple murine acute inflammatory settings. Collectively, our findings present GPR84 as a novel physiological regulator of immune cell extravasation that is amenable to therapeutic targeting for modulating leukocyte infiltration into inflamed tissues. SummaryHere we identify the GPR84 family of GPCRs as key regulators of effective immune cell extravasation in vivo. Mechanistically, through integrating genetically tractable Drosophila and murine in vivo models, we show how leukocyte GPR84 supports dynamic Rho-dependent detachment of stretched uropods as these cells exit vessels.

immunology↗

bioRxiv2026

Impact of impaired endogenous neurosteroidogenesis on outcomes following chronic alcohol exposure.

Alcohol use disorder is a major public health concern worldwide and there is a high comorbidity with psychiatric disorders. The basolateral amygdala (BLA) has been implicated in both mood and alcohol use disorders; however, the mechanisms contributing to the shared pathophysiology remain unknown. Extensive evidence indicates that ethanol modulates GABAergic signaling in the BLA, including actions on neurosteroid-sensitive, extrasynaptic {delta} subunit-containing GABAA receptors (GABAARs), which has been suggested to mediate many of the behavioral effects. In fact, several studies have suggested that 5-reduced neurosteroids, such as allopregnanolone, may mediate some of the behavioral effects of alcohol. Here we demonstrate that chronic intermittent ethanol (CIE) exposure impairs endogenous neurosteroidogenesis via downregulation of key neurosteroidogenic enzymes, 5-reductase type 1 and type 2. To examine the impact of impaired endogenous neurosteroidogenesis of the behavioral consequences of chronic alcohol exposure, including withdrawal-induced anxiety and increased alcohol consumption, we used CRISPR/Cas9 mediated knockdown of 5-reductase in the BLA. Reduced expression of 5-reductase in the BLA did not impact post-CIE alcohol intake or anxiety-like behaviors during withdrawal, perhaps because endogenous neurosteroidogenesis is already impaired following CIE. Therefore, we examined the impact of enhancing neurosteroid levels, treating mice post-CIE with SGE-516, a synthetic GABAAR positive allosteric modulator, which increased voluntary alcohol intake. These findings implicate endogenous neurosteroidogenesis in behavioral outcomes associated with withdrawal from chronic alcohol exposure. Further, this study suggests that targeting endogenous neurosteroidogenesis may be a novel and useful therapeutic target.

neuroscience↗

bioRxiv2025

Analysis of SIV Spatiotemporal Dissemination Patterns in Rhesus Macaques During Early Rectal Transmission Demonstrates Systemic Infection Does Not Require Viral Local Amplification at the Entry Portal

Receptive anal sex is a dominant mode of HIV-1 (HIV) transmission, especially among men who have sex with men (MSM). However, the early events during HIV rectal transmission are not well understood and many questions remain, such as, does virus local amplification at the entry portal require for viral distal seeding? What is the spatiotemporal dissemination pattern across whole body? How do three viral forms, i.e., cell-free virus (VCF), cell-associated virus (VCA), and follicular dendritic cell-trapped virus (VFDC), evolve during early infections? To close this knowledge gap, we comprehensively examined rectum, draining lymph nodes (dLN) and distal lymph nodes (disLN), as well as non-lymphoid organs of brain, lungs, and liver of Indian rhesus macaques (RMs) at the early time points following intrarectal SIVmac251 inoculation (1, 2, 3, 4, 6, 10 14, 28 day post inoculation, dpi). Our findings demonstrated SIV rapidly disseminates to distant tissues and organs (<=1 dpi) and virus local amplification in rectum and dLN is not required for viral distal seeding for the establishment of systemic infection, viral forms shift from VCF and VCA to VFDC accompanying from T cell zones into B cell follicles. Collectively, these findings indicate that an effective HIV vaccine needs to induce immune protection both locally at sites of viral entry and systemically.

immunology↗

bioRxiv2025

Germline-targeting HIV immunogen induces cross-neutralizing antibodies in outbred macaques

Germline-targeting-(GT) is a promising strategy to activate rare broadly neutralizing antibody (bnAb)-producing B cells against HIV, but induction of such responses in outbred animals has not been achieved. Using antibody-guided structure-based design, we engineered a germline-targeting trimer immunogen Q23-APEX-GT2 that primes diverse V2-apex bnAb precursors. Q23-APEX-GT2 efficiently activated V2-apex-specific B cells in humanized knock-in mice and consistently elicited immunofocused antibody responses in rhesus macaques, priming multiple long CDRH3-loop bnAb-B cell lineages. Monoclonal antibodies from immunized macaques exhibited broad heterologous HIV trimer binding and cross-neutralization. Atomic-level structural studies confirmed precise epitope targeting and revealed CDRH3-paratope configurations that mirrored those of human V2-apex bnAbs. This study provides proof-of-principle for successful priming and maturation of authentic V2-apex bnAb precursors in outbred macaques, underscoring the potential of V2-apex-targeted vaccines. HIGHLIGHTSO_LIEngineered Q23-APEX-GT2 trimer to stimulate diverse V2-apex bnAb B cell precursors C_LIO_LIQ23-APEX-GT2 primed rare V2-apex bnAb B cells in mice and outbred rhesus macaques C_LIO_LIQ23-APEX-GT2 elicited immunofocused antibody responses and diverse V2-apex B cell lineages with desirable long-CDRH3 paratope properties C_LIO_LIQ23-APEX-GT2 alone induced V2-apex antibodies with broad HIV trimer binding and modest neutralization breadth C_LIO_LIStructural analysis confirmed bnAb site targeting, mirroring human and rhesus V2-apex bnAbs C_LI

immunology↗

bioRxiv2025

Env-antibody coevolution identifies B cell priming as the principal bottleneck to HIV-1 V2 apex broadly neutralizing antibody development

Broadly neutralizing antibodies (bNAbs) are rarely elicited during HIV-1 infection. To identify obstacles to bNAb development, we longitudinally studied 122 rhesus macaques infected by one of 16 different simian-human immunodeficiency viruses (SHIVs). We identified V2 apex as the most common bNAb target and a subset of Envs that preferentially elicited these antibodies. In 10 macaques, we delineated Env-antibody coevolution from B cell priming to bNAb development. Antibody phylogenies revealed permissive developmental pathways guided by evolving Envs that contained few mutations in or near the V2 apex C-strand, which were a sensitive indicator of apex-targeted responses. The absence of such mutations reflected a failure in bNAb priming. These results indicate that efficiency of B cell priming, and not complexities in Env-guided affinity maturation, is the primary obstacle to V2 apex bNAb elicitation in SHIV-infected macaques and identify specific HIV-1 Envs to advance as novel vaccine platforms. One sentence summaryB cell priming is the primary bottleneck to HIV-1 V2 apex bNAb elicitation.

immunology↗

bioRxiv2024

Evolutionary dynamics at the leading edge ofbiological invasions

Empirical evidence shows that evolution may take place during species range expansion. Indeed, dispersal ability tends to be selected for at the leading edge of invasions, ultimately increasing a species spreading speed. However, for organisms across many different taxa, higher dispersal comes at the cost of fitness, producing evolutionary trade-offs at the leading edge. Using reaction-diffusion equations and adaptive dynamics, we provide new insights on how such evolutionary processes take place. We show how evolution may drive phenotypes at the leading edge to maximize the asymptotic spreading speed, and conditions under which phenotypic plasticity in dispersal is selected for under different dispersal-reproduction trade-off scenarios. We provide some possible future research directions and other systems where the framework can be applied.

evolutionary biology↗

bioRxiv2024

Polyploid cancer cells reveal signatures of chemotherapy resistance

Therapeutic resistance in cancer significantly contributes to mortality, with many patients eventually experiencing recurrence after initial treatment responses. Recent studies have identified therapy-resistant large polyploid cancer cells in patient tissues, particularly in late-stage prostate cancer, linking them to advanced disease and relapse. Here, we analyzed bone marrow aspirates from 44 advanced prostate cancer patients and found the presence of circulating tumor cells with increased genomic content (CTC-IGC) was significantly associated with poorer progression- free survival. Single cell copy number profiling of CTC-IGC displayed clonal origins with typical CTCs, suggesting complete polyploidization. Induced polyploid cancer cells from PC3 and MDA-MB-231 cell lines treated with docetaxel or cisplatin were examined through single cell DNA sequencing, RNA sequencing, and protein immunofluorescence. Novel RNA and protein markers, including HOMER1, TNFRSF9, and LRP1, were identified as linked to chemotherapy resistance. These markers were also present in a subset of patient CTCs and associated with recurrence in public gene expression data. This study highlights the prognostic significance of large polyploid tumor cells, their role in chemotherapy resistance, and their expression of markers tied to cancer relapse, offering new potential avenues for therapeutic development.

cancer biology↗

bioRxiv2024

Recent Bovine HPAI H5N1 Isolate is Highly Virulent for Mice, Rapidly Causing Acute Pulmonary and Neurologic Disease

The highly pathogenic avian influenza (HPAI) A(H5N1) clade 2.3.4.4b viruses, responsible for the current outbreak in dairy cows in the United States, pose a significant animal and public health threat. In this study, we compared disease progression and pathology of three recent clade 2.3.4.4b isolates derived from a cow, mountain lion, and mink to a human HPAI A(H5N1) isolate from Vietnam in mice. Inoculation of C57BL/6J and BALB/c mice with all four HPAI A(H5N1) isolates resulted in comparable levels of virus replication in the lung inducing severe respiratory disease. C57BL/6J mice infected with the bovine isolate also developed high virus titers in the brain, resulting in a significant pro-inflammatory cytokine response and neurologic disease. Our findings suggest the recent bovine isolate possesses enhanced respiratory and neuroinvasive/neurovirulent properties causing fatal respiratory and neurologic disease in C57BL/6J mice.

microbiology↗

bioRxiv2023

Coupling mountain pine beetle and forest population dynamics predicts transient outbreaks that are likely to increase in number with climate change

Mountain pine beetle (MPB) in Canada have spread well beyond their historical range. Accurate modelling of the long-term dynamics of MPB is critical for assessing the risk of further expansion and informing management strategies, particularly in the context of climate change and variable forest resilience. Most previous models have focused on capturing a single outbreak without tree replacement. While these models are useful for understanding MPB biology and outbreak dynamics, they cannot accurately model long-term forest dynamics. Past models that incorporate forest growth tend to simplify beetle dynamics. We present a new model that couples forest growth to MPB population dynamics and accurately captures key aspects of MPB biology, including a threshold for the number of beetles needed to overcome tree defenses and beetle aggregation that facilitates mass attacks. These mechanisms lead to a demographic Allee effect, which is known to be important in beetle population dynamics. We show that as forest resilience decreases, a fold bifurcation emerges and there is a stable fixed point with a non-zero MPB population. We derive conditions for the existence of this equilibrium. We then simulate biologically relevant scenarios and show that the beetle population approaches this equilibrium with transient boom and bust cycles with period related to the time of forest recovery. As forest resilience decreases, the Allee threshold also decreases. Thus, if host resilience decreases under climate change, for example under increased stress from drought, then the lower Allee threshold makes transient outbreaks more likely to occur in the future. Statements and DeclarationsO_ST_ABSCompeting interestsC_ST_ABSThe authors declare no competing interests. Data availability statementData sharing is not applicable to this article as no datasets were generated or analysed during the current study. Code to produce the figures is available at github.com/micbru/MPBModel/.

ecology↗

bioRxiv2023

Identifying signals of memory from observations of animal movements in Plato's cave

Incorporating memory (i.e., some notion of familiarity or experience with the landscape) into models of animal movement is a rising challenge in the field of movement ecology. The recent proliferation of new methods offers new opportunities to understand how memory influences movement. However, there are no clear guidelines for practitioners wishing to parameterize the effects of memory on moving animals. We review approaches for incorporating memory into Step-Selection Analyses (SSAs), a frequently used movement modeling framework. Memory-informed SSAs can be constructed by including spatial-temporal covariates (or maps) that define some aspect of familiarity (e.g., whether, how often, or how long ago the animal visited different spatial locations) derived from long-term telemetry data. We demonstrate how various familiarity covariates can be included in SSAs using a series of coded examples in which we fit models to wildlife tracking data from a wide range of taxa. We discuss how these different approaches can be used to address questions related to whether and how animals use information from past experiences to inform their future movements. We also highlight challenges and decisions that the user must make when applying these methods to their tracking data. By reviewing different approaches and providing code templates for their implementation, we hope to inspire practitioners to investigate further the importance of memory in animal movements using wildlife tracking data.

ecology↗

bioRxiv2023

Witnessed trauma exposure induces fear in mice through a reduction in endogenous neurosteroid synthesis

Neurosteroids have been implicated in the pathophysiology of post-traumatic stress disorder (PTSD). Allopregnanolone is reduced in subsets of individuals with PTSD and has been explored as a novel treatment strategy. Both direct trauma exposure and witnessed trauma are risk factors for PTSD; however, the role of neurosteroids in the behavioral outcomes of these unique experiences has not been explored. Here we investigate whether observational fear is associated with a reduced capacity for endogenous neurosteroidogenesis and the relationship with behavioral outcomes. We demonstrate that both mice directly subjected to the threat (foot shocks) and those witnessing the threat have decreased plasma levels of allopregnanolone. The expression of a key enzyme involved in endogenous neurosteroid synthesis, 5-reductase type 2, is decreased in the basolateral amygdala (BLA), which is a major emotional processing hub implicated in PTSD. We demonstrate that knockdown of 5-reductase type 2 exaggerates the behavioral expression of fear in response to witnessed trauma, whereas treatment with an exogenous, synthetic neuroactive steroid GABAA receptor PAM with molecular pharmacology similar to allopregnanolone (SGE-516 [tool compound]) decreases the behavioral response to observational fear. These data implicate impaired endogenous neurosteroidogenesis in the pathophysiology of threat exposure, both direct and witnessed. Further, these data suggest that treatment with exogenous 5-reduced neurosteroids or targeting endogenous neurosteroidogenesis may be beneficial for the treatment of individuals with PTSD, whether resulting from direct or witnessed trauma.

neuroscience↗

bioRxiv2023

Neuro-Regenerative Behavior of Adipose-Derived Stem Cells in Aligned Collagen I Hydrogels

Peripheral nerve injuries persist as a major clinical issue facing the US population and can be caused by stretch, laceration, or crush injuries. Small nerve gaps are simple to treat, and the nerve stumps can be reattached with sutures. In longer nerve gaps, traditional treatment options consist of autografts, hollow nerve guidance conduits, and, more recently, manufactured fibrous scaffolds. These manufactured scaffolds often incorporate stem cells, growth factors, and/or extracellular matrix (ECM) proteins to better mimic the native environment but can have issues with homogenous cell distribution or uniformly oriented neurite outgrowth in scaffolds without fibrous alignment. Here, we utilize a custom device to fabricate collagen I hydrogels with aligned fibers and encapsulated adipose-derived mesenchymal stem cells (ASCs) for potential use as a peripheral nerve repair graft. Analysis of these scaffolds in vitro revealed heightened therapeutic secretome from ASCs, ECM deposition, and dorsal root ganglia (DRG) neurite outgrowth along the axis of fiber alignment. Our platform serves as an in vitro testbed platform to assess neuro-regenerative potential of ASCs in aligned collagen fiber scaffolds and may provide guidance on next-generation nerve repair scaffold design.

bioengineering↗