Biology subjects

King, B.

Publications and source records attributed to King, B..

12 recordsLinked to original sources

bioRxiv2026

Sleep Spindle-Locked Targeted Memory Reactivation Enhances Declarative Memory Consolidation

Study ObjectivesSleep spindles are implicated in memory consolidation. Yet direct evidence linking spindle dynamics to declarative memory outcomes remains limited. We thus tested whether targeted memory reactivation (TMR) time-locked to sleep spindles enhances declarative memory, and whether the temporal organization of stimulated spindles-trains versus isolated events-is selectively associated with distinct memory outcomes. MethodsTwenty-eight healthy young adults learned image locations from two categories (animals, clothing) in a grid, each paired with a distinct auditory cue. During overnight NREM sleep, one cue was replayed time-locked to spindles detected in real-time using a closed-loop system (TMR condition); the other served as the non-reactivated control (No-TMR condition). Category-cue assignment was counterbalanced. Post-sleep recall, recognition accuracy, and movement time were assessed. ResultsRecall accuracy was significantly higher in the TMR than the No-TMR condition (93.96% vs. 90.61%, p = .024), whereas recognition accuracy (p = .139) and movement time (p = .651) did not differ. Stimulation intensity within spindle trains correlated with the TMR effect on recall (Spearman {rho} = .531, p = .004), whereas the proportion of isolated spindle stimulations correlated with the TMR effect on recognition ({rho} = .563, p = .002). Cross-associations were not significant. ConclusionsSpindle-locked TMR enhances recall-based declarative memory retention. The selective association between spindle temporal clustering and memory outcomes suggests that train-embedded and isolated spindles support different aspects of memory consolidation, highlighting spindle temporal context as a functionally relevant dimension of sleep-dependent memory processing.

neuroscience↗

bioRxiv2026

Posterior simulation-based calibration tests of phylogenetic dating methods

Simulation-based calibration (SBC) checking is a method to ensure that the inference machinery for a Bayesian statistical analysis is functioning in a correct and unbiased manner. Typically, SBC begins with sampling parameter values from the model priors (prior SBC). However, it has been shown that prior SBC can miss problems when these manifest only in certain regions of parameter space. In phylogenetics, this is relevant not only because of the vastness of tree and parameter space, but also because many phylogenetic analyses involve some degree of model misspecification. Posterior SBC is a recently developed method for checking that the inference algorithms function correctly for a given empirical dataset. Here I use posterior SBC to test the implementation of phylogenetic dating methods in the inference software BEAST 2. I test both the tip-dated approach, employing an Indo-European vocabulary dataset, and the node-dated approach, employing a molecular rRNA dataset of Tabanidae (horseflies). In both cases, posterior SBC tests indicate good calibration. Despite this, posterior predictive datasets simulated from the posterior distribution provided no further increase in the precision of node age estimates compared to the original posterior, a result consistent with previous literature showing fundamental theoretical limits to the identifiability of node ages. Nevertheless, these results suggest that phylogenetic dating methods in BEAST 2 are not biased by problems with the inference machinery, thereby increasing confidence in results obtained using these methods.

evolutionary biology↗

bioRxiv2026

Contingency Inverts Mammalian Herbivore Evolution in Australia

The rise of Neogene herbivores with high-crowned (hypsodont) molar teeth has been viewed as a mostly predictable response to abrasive grazing diets. Using kangaroos, an isolated marsupial radiation, we show that the ancestral vertical slicing function of grazing kangaroo molars prompted heavy investment from the late Miocene in thickened enamel, rather than hypsodonty. Grazing kangaroo enamel thickness overlaps some robust hominins, evincing an eclectic, thick-enamelled grazer guild. The success of vertically-chewing marsupials contrasts with their placental counterparts, which were overwhelmingly replaced by transversely-chewing ungulates. This inversion is explained by the pre-grassland extinction of most transversely-chewing marsupials, and the crucial advent of thick enamel. These results challenge the determinism of the browser-grazer transition, and implicate extinction, and ensuing innovation, as causes of unpredictability in evolution.

paleontology↗

bioRxiv2025

Outer membrane vesicles from Bacteroides fragilis contain coding and non-coding small RNA species that modulate inflammatory signaling in intestinal epithelial cells.

Alterations to the community structure and function of the microbiome are associated with changes to host physiology, including immune responses. However, the contribution of microbe-derived RNAs carried by outer membrane vesicles (OMVs) to host immune responses remain unclear. This study investigated the role of OMVs and OMV-associated small RNA (sRNA) species from pathogenic and commensal Bacteroides fragilis (ETBF and NTBF respectively) in eliciting different immune responses from intestinal epithelial cells. To distinguish the differences in the sRNA profiles of the two strains and their OMVs, RNA-seq, qRT-PCR, and northern blotting were conducted to identify enrichment of discrete sRNA species in OMVs, which were also differentially expressed between the two strains. Specifically, both coding and non-coding RNAs were enriched in OMVs from NTBF and ETBF, with BF9343_RS22680 and BF9343_RS17870 being significantly enriched in ETBF OMVs compared to NTBF. To understand the effects of OMVs on pattern recognition receptors, reporter cells of Toll-like receptor (TLR) activation were treated with OMVs, demonstrating activation of TLRs 2, 3, and 7. Treatment of Caco-2 and HT29-MTX cells with OMVs demonstrated increased expression of IL-8. Surprisingly, we discovered that degradation of RNase-accessible RNAs within ETBF OMVs, but not NTBF OMVs, resulted in vesicles with enhanced capacity to stimulate IL-8 expression, indicating that these extravesicular RNAs exert an immunosuppressive effect. This suggests a dual role for OMV-associated RNAs in modulating host immune responses, with implications for both bacterial pathogenesis and therapeutic applications. Graphical Abstract

molecular biology↗

bioRxiv2025

Cutaneous lupus features specialized stromal niches and altered retroelement expression

Cutaneous Lupus is an inflammatory skin disease causing highly morbid inflamed skin and hair loss. In order to investigate the pathophysiology of cutaneous lupus, we performed single-cell RNA and spatial sequencing of lesional and non-lesional cutaneous lupus skin compared to healthy controls. Pathway enrichment analyses of lesional keratinocytes revealed elevated responses to type I interferon, type II interferon, tumor necrosis factor, and apoptotic signaling. Detailed clustering demonstrated unique fibroblasts specific to lupus skin with likely roles in inflammatory cell recruitment and fibrosis. We also evaluated the association of retroelement expression with type I interferons in the skin. We observed increased retroelement expression which correlated with interferon-stimulated genes across multiple cell types. Moreover, we saw elevated expression of genes involved in RIG-I and cGAS-STING pathways, which transduce elevated nucleic acid signals. Treatment of active cutaneous lupus with Anifrolumab reduced RIG-I and cGAS-STING pathways in addition to the most abundant retroelement family, L2b. Our studies better define type I interferon-mediated immunopathology in cutaneous lupus and identify an association between retroelement expression and interferon signatures in cutaneous lupus.

immunology↗

bioRxiv2024

Carbon-conserving Bioproduction of Malate in an E. coli-based Cell-Free System

Formate, a biologically accessible form of CO2, has attracted interest as a renewable feedstock for bioproduction. However, approaches are needed to investigate efficient routes for biological formate assimilation due to its toxicity and limited utilization by microorganisms. Cell-free systems hold promise due to their potential for efficient use of carbon and energy sources and compatibility with diverse feedstocks. However, bioproduction using purified cell-free systems is limited by costly enzyme purification, whereas lysate-based systems must overcome loss of flux to background reactions in the cell extract. Here, we engineer an E. coli-based system for an eight-enzyme pathway from DNA and incorporate strategies to regenerate cofactors and minimize loss of flux through background reactions. We produce the industrial di-acid malate from glycine, bicarbonate, and formate by engineering the carbon-conserving reductive TCA and formate assimilation pathways. We show that in situ regeneration of NADH drives metabolic flux towards malate, improving titer by 15-fold. Background reactions can also be reduced 6-fold by diluting the lysate following expression and introducing chemical inhibitors of competing reactions. Together, these results establish a carbon-conserving, lysate-based cell-free platform for malate production, producing 64 M malate after 8 hours. This system conserves 43% of carbon otherwise lost as CO2 and incorporates 0.13 mol CO2 equivalents/mol glycine fed. Finally, techno-economic analysis of cell-free malate production from formate revealed that the high cost of lysate is a key challenge to the economic feasibility of the process, even assuming efficient cofactor recycling. This work demonstrates the capabilities of cell-free expression systems for both the prototyping of carbon-conserving pathways and the sustainable bioproduction of platform chemicals. HighlightsO_LISuccessfully engineered the carbon-conserving reductive TCA and formate assimilation pathways in a lysate-based cell-free system for production of the C4 industrial di-acid malate from C1 and C2 feedstocks. C_LIO_LIAchieved a 6-fold reduction in competition from the endogenous cell-free metabolism by blocking TCA activity using small-molecule inhibitors and lysate dilution. C_LIO_LIIncreased accumulation of malate by 15-fold in a single-step reaction using cell-free expression of an enzymatic cofactor regeneration system. C_LIO_LITechno-economic analysis identified routes for economically feasible production of malate from renewable feedstocks in a cell-free system by improving conversion efficiency and reducing lysate cost. C_LI Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=161 SRC="FIGDIR/small/623433v1_ufig1.gif" ALT="Figure 1"> View larger version (29K): org.highwire.dtl.DTLVardef@3c89adorg.highwire.dtl.DTLVardef@72d9b3org.highwire.dtl.DTLVardef@327e2eorg.highwire.dtl.DTLVardef@fa0964_HPS_FORMAT_FIGEXP M_FIG C_FIG

synthetic biology↗

bioRxiv2024

Impaired online and enhanced offline motor sequence learning in individuals with Parkinson's disease

Whereas memory consolidation research has traditionally focused on longer temporal windows (i.e., hours to days) following an initial learning episode, recent research has also examined the functional significance of the shorter rest epochs commonly interspersed with blocks of task practice (i.e., "micro-offline" intervals on the timescale of seconds to minutes). In the motor sequence learning domain, evidence from young, healthy individuals suggests that micro-offline epochs afford a rapid consolidation process that is supported by the hippocampus. Consistent with these findings, amnesic patients with hippocampal damage were recently found to exhibit degraded micro-offline performance improvements. Interestingly, these offline losses were compensated for by larger performance gains during online practice. Given the known role of the striatum in online motor sequence learning, we hypothesized that individuals with dysfunction of the striatal system would exhibit impaired online, yet enhanced micro-offline, learning (i.e., a pattern of results opposite to those observed in patients with hippocampal lesions). We tested this hypothesis using Parkinsons disease (PD) as a model of striatal dysfunction. Forty-two drug-naive individuals (men and women) with a clinical diagnosis of unilateral PD and 30 healthy control subjects completed a motor sequence learning paradigm. Individuals with PD exhibited deficits during online task practice that were paralleled by greater improvements over micro-offline intervals. This pattern of results could not be explained by disease-related deficits in movement execution. These data suggest that striatal dysfunction disrupts online learning, yet total learning remains unchanged because of greater micro-offline performance improvements that potentially reflect hippocampal-mediated compensatory processes. Significance StatementThe short rest intervals commonly interspersed between periods of active task engagement have traditionally been employed to minimize the build-up of fatigue. There is recent evidence, however, suggesting that these rest epochs may play an active role in motor learning and memory processes and the hippocampus appears to be a critical brain region supporting this rapid "offline" learning. Here, we show that individuals with Parkinsons disease, a movement disorder characterized by dysfunction in the basal ganglia including the striatum, exhibit deficits during active task practice but greater learning over the interspersed offline intervals. Results potentially suggest that the relatively intact hippocampus may help compensate for motor sequence learning deficits linked to a disrupted striatal system in Parkinsons disease.

neuroscience↗

bioRxiv2024

A pumpless and tubeless microfluidic device enables extended in vitro development of Cryptosporidium parvum

The enteric parasite Cryptosporidium remains a treatment challenge for drinking water utilities globally due to its resistance to chlorine disinfection. However, the lack of an in vitro culture system for Cryptosporidium that is both cost-effective and reliable remains a key bottleneck in Cryptosporidium research. Here we report that the microfluidic culture of HCT-8 cells under fluid shear stress enables the extended development of Cryptosporidium parvum. Specifically, the growth of C. parvum in a user-friendly pumpless microfluidic device was assessed using immunofluorescence assays, scanning electron microscopy and quantitative PCR, which revealed that development peaked at six days post-infection but continued for ten days in total. Oocysts produced within the microfluidic device were infective to fresh HCT-8 monolayers, however these oocysts were only present at low levels. We anticipate that such microfluidic approaches will facilitate a wide range of in vitro studies on Cryptosporidium and may have the potential to be further developed as a routine infectivity assessment tool for the water industry.

microbiology↗

bioRxiv2023

Multi-spectral Fluorescent Reporter Influenza A Viruses Allow for in vivo Studies of Innate Immune Function in Zebrafish

Influenza virus infection can cause severe respiratory disease and is estimated to cause millions of illnesses annually. Studies of the contribution of the innate immune response to influenza A virus (IAV) to viral pathogenesis may yield new antiviral strategies. Zebrafish larvae are useful models to study the innate immune response to pathogens, including IAV, in vivo. Here, we demonstrate how Color-flu, four fluorescent IAV strains originally developed for mice, can be used to study host-virus interactions by simultaneously monitoring virus particles, neutrophils, and macrophages in vivo. Using this model, we show how the angiotensin-converting enzyme inhibitor, ramipril, and mitophagy inhibitor, MDIVI-1, improved survival, decreased viral burden, and improved the respiratory burst response to IAV infection. The Color-flu zebrafish model of IAV infection is complementary to other models as it is the only model where interactions between virus particles and host cells in an intact vertebrate can be visualized in vivo.

immunology↗

bioRxiv2021

Inducible and reversible inhibition of miRNA-mediated gene repression in vivo

Although virtually all gene networks are predicted to be controlled by miRNAs, the contribution of this important layer of gene regulation to tissue homeostasis in adult animals remains unclear. Gain and loss of function experiments have provided key insights into the specific function of individual miRNAs, but effective genetic tools to study the functional consequences of global inhibition of miRNA activity in vivo are lacking. Here we report the generation and characterization of a genetically engineered mouse strain in which miRNA-mediated gene repression can be reversibly inhibited without affecting miRNA biogenesis or abundance. We demonstrate the usefulness of this strategy by investigating the consequences of acute inhibition of miRNA function in adult animals. We find that different tissues and organs respond differently to global loss of miRNA function. While miRNA-mediated gene repression is essential for the homeostasis of the heart and the skeletal muscle, it is largely dispensable in the majority of other organs. Even in tissues where it is not required for homeostasis, such as the intestine and hematopoietic system, miRNA activity can become essential during regeneration following acute injury. These data support a model where many metazoan tissues primarily rely on miRNA function to respond to potentially pathogenic events.

molecular biology↗

bioRxiv2019

Bayesian Tip-dated Phylogenetics: Topological Effects, Stratigraphic Fit and the Early Evolution of Mammals

ABSTRACTThe incorporation of stratigraphic data into phylogenetic analysis has a long history of debate, but is not currently standard practice for palaeontologists. Bayesian tip-dating (or morphological clock) phylogenetic methods have returned these arguments to the spotlight, but how tip-dating affects the recovery of evolutionary relationships has yet to be fully explored. Here we show, through analysis of several datasets with multiple phylogenetic methods, that topologies produced by tip-dating are outliers when compared to topologies produced by parsimony and undated Bayesian methods, which retrieve broadly similar trees. Unsurprisingly, trees recovered by tip-dating have better fit to stratigraphy than trees recovered by other methods, due to trees with better stratigraphic fit being assigned a higher prior probability. Differences in stratigraphic fit and tree topology between tip-dating and other methods appear to be concentrated in parts of the tree with weaker character signal and a stronger influence of the prior, as shown by successive deletion of the most incomplete taxa from a sauropod dataset. Tip-dating applied to Mesozoic mammals firmly rejects a monophyletic Allotheria, and strongly supports diphyly of haramiyidans, with the late Triassic Haramiyavia and Thomasia forming a clade with tritylodontids, which is distant from the middle Jurassic euharamiyidans. This result is not sensitive to the controversial age of the eutherian Juramaia. A Test of the age of Juramaia using a less restrictive prior reveals strong support from the data for an Early Cretaceous age. Our results suggest that tip-dating incorporates stratigraphic data in an intuitive way, with good stratigraphic fit a prior expectation that can be overturned by strong evidence from character data.View Full Text

paleontology↗

bioRxiv2017

ProbAnnoWeb and ProbAnnoPy: probabilistic annotation and gap-filling of metabolic reconstructions

SummaryGap-filling is a necessary step to produce quality genome-scale metabolic reconstructions capable of flux-balance simulation. Most available gap-filling tools use an organism-agnostic approach, where reactions are selected from a database to fill gaps without consideration of the target organism. Conversely, our likelihood based gap-filling with probabilistic annotations selects candidate reactions based on a likelihood score derived specifically from the target organisms genome. Here, we present two new implementations of probabilistic annotation and likelihood based gap-filling: a web service called ProbAnnoWeb, and a standalone python package called ProbAnnoPy.\n\nAvailability and ImplementationOur tools are available as a web service with no installation needed (ProbAnnoWeb), available at http://probannoweb.systemsbiology.net, and as a local python package implementation (ProbAnnoPy), available for download at http://github.com/PriceLab/probannopy.\n\nContacthttp://Evangelos.Simeonidis@systemsbiology.org; http://Nathan.Price@systemsbiology.org

systems biology↗