Biology subjects

Urban, N.

Publications and source records attributed to Urban, N..

9 recordsLinked to original sources

bioRxiv2026

Plasmodium berghei liver stages establish a damage-mimicking vacuole to hijack host ER membrane contact site machinery for lipid uptake

Plasmodium liver stage parasites undergo massive intracellular replication and therefore require extensive acquisition of host-derived lipids. How parasites coordinate lipid supply at the host-parasite interface, however, remains poorly understood. Here, we show that the Plasmodium berghei parasitophorous vacuole membrane (PVM) selectively mimics features of damaged endolysosomal membranes, including dynamic LC3-positive membrane tubules and PI4K2A-dependent PI(4)P accumulation, while lacking canonical damage markers including ESCRT components and galectins. This damage-mimicking membrane state drives OSBP recruitment and is associated with formation of VAPA/B-positive ER-PVM membrane contact sites. Disruption of VAPA/B or OSBP impaired PVM integrity and parasite survival, while OSBP depletion reduced cholesterol accumulation at the PVM. Together, our findings suggest that liver stage parasites exploit host lysosome repair-like pathways to redirect host lipids toward parasite growth and intracellular survival. These results redefine the PVM as an active metabolic interface that enables host lipid acquisition rather than merely serving as a protective barrier.

microbiology↗

bioRxiv2024

Ideal efficacy photoswitches for TRPC4/5 channels harness high potency for spatiotemporally-resolved control of TRPC function in live tissues

Directly probing the endogenous biological roles of target proteins with high spatial and temporal resolution, as non-invasively and reproducibly as possible, is a shared conceptual goal for research across many fields, as well as for targeted therapies. Here we describe the rational conceptual design and test-case practical implementation of a photopharmacological paradigm to empower high-performance photomodulation studies in vivo. TRPC4/5 ion channels are involved in many spatiotemporally resolved circuits, from pain and anxiety, to reproductive signaling, digestion, and obesity. To unpick their biology requires spatiotemporally precise tools, which were lacking. We developed "ideal efficacy photoswitch" ligands to control their diverse functions in situ. These E{leftrightarrows}Z-photoswitchable ligands bias TRPC[4]/5 channel activity with exquisite photocontrol, from strong agonism under 360 nm, to low agonism at 385 nm, to strong antagonism at 410-460 nm. Cryo-EM structures of both TRPC4 and TRPC5 with both Z-agonists and E-antagonists support the rationale for efficacy switching through competitive E/Z isomer binding. Crucially, since the E/Z ratio is exclusively determined by the light wavelength applied, their channel photocontrol is exclusively wavelength-dependent, yet drug-concentration-independent: so is reproducible from cell culture to >millimetre-depth tissues. Indeed, we were able to photocontrol both direct and downstream TRPC4/5 biology in cell lines or primary cells in culture, from calcium flux, to primary neuron excitability and adrenaline release; and even in tissues, photoswitching small intestine motility and peristalsis. The TRPC4/5 ligands we develop will thus unlock a range of high-precision investigations in TRP biology. More broadly, we propose that the success of this efficacy photoswitch program, from concept to tissue level translation, is mainly a consequence of how biology has evolved proteins for efficacy control. We therefore foresee that a variety of functionally responsive protein targets, not only sensory and signaling ion channels and receptors, will be amenable to similarly high-performance photocontrol even in vivo, if a new generation of reagent development adopts this paradigm of ideal efficacy photoswitching. Table of Contents Graphic O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=84 SRC="FIGDIR/small/602451v1_ufig1.gif" ALT="Figure 1"> View larger version (24K): org.highwire.dtl.DTLVardef@1f8e527org.highwire.dtl.DTLVardef@18c72d0org.highwire.dtl.DTLVardef@1c5d648org.highwire.dtl.DTLVardef@177203d_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗

bioRxiv2023

Pharmacodynamic model of PARP1 inhibition and global sensitivity analyses can lead to cancer biomarker discovery

Pharmacodynamic models provide inroads to understanding key mechanisms of action and may significantly improve patient outcomes in cancer with improved ability to determine therapeutic benefit. Additionally, these models may also lead to insights into potential biomarkers that can be utilized for prediction in prognosis and therapeutic decisions. As an example of this potential, here we present an advanced computational Ordinary Differential Equation (ODE) model of PARP1 signalling and downstream effects due to its inhibition. The model has been validated experimentally and further evaluated through a global sensitivity analysis. The sensitivity analysis uncovered two model parameters related to protein synthesis and degradation rates that were also found to contribute the most variability to the therapeutic prediction. Because this variability may define cancer patient subpopulations, we interrogated genomic, transcriptomic, and clinical databases, to uncover a biomarker that may correspond to patient outcomes in the model. In particular, GSPT2, a GTPase with translation function, was discovered and if mutations serve to alter catalytic activity, its presence may explain the variability in the models parameters. This work offers an analysis of ODE models, inclusive of model development, sensitivity analysis, and ensuing experimental data analysis, and demonstrates the utility of this methodology in uncovering biomarkers in cancer. Author summaryBecause biochemical reaction networks are complex, dynamic, and typically provide output that results from non-linear interactions, mathematical models of such offer insight into cell function. In the clinic, models including drug action further their usefulness in that they may predict therapeutic outcome and other useful markers such as those for prognosis. In this study, we report a model of drug action that targets a critical protein, that when inhibited, promotes tumor cell death and documented remissions. Because all patients do not respond to the described treatment, a means to find cancer patient subpopulations that might benefit continues to be a challenge. Therefore, we analyzed the pharmacodynamic model by defining the parameters of the greatest variability and interrogated genomic, transcriptomic, and clinical cohort databases with this information and discovered a novel biomarker associated with prognosis in some ovarian and uterine cancer patients and separately, associated with the potential to respond to treatment.

bioinformatics↗

bioRxiv2022

Adult neural stem cells and neurogenesis are resilient to intermittent fasting

Intermittent fasting (IF) is a promising non-pharmacological strategy to counteract ageing which has been shown to increase the number of adult-born neurons in the dentate gyrus of mice. However, it is still unclear which steps of the adult neurogenesis process are regulated by IF. The number of adult neural stem cells (NSCs) decreases with age in an activation-dependent manner. To counteract the loss of the stem cell pool, adult NSCs are mostly found in an inactive, quiescent state which ensures their long-term maintenance. We aimed to determine if and how IF impacts the activity and maintenance of adult NSCs in the hippocampus. We chose an every-other-day fasting protocol with food re-administration at night, which we found effectively induces fasting features and preserves the circadian activity pattern of mice. To determine the effects of IF on NSCs and all following steps in the neurogenic lineage, we combined fasting with lineage tracing and label retention assays. We found that IF does not affect NSC activation or maintenance. Contrary to previous reports, we also found that IF does not increase hippocampal neurogenesis. We obtained the same results regardless of strain, sex, diet length, tamoxifen administration or new-born neuron identification method. Our data suggest that NSCs maintain homeostasis upon IF and that this intervention is not a reliable strategy to increase adult neurogenesis.

neuroscience↗

bioRxiv2021

OptoAssay - Light-controlled Dynamic Bioassay Using Optogenetic Switches

Circumventing the limitations of current bioassays, we introduce the first light-controlled assay, the OptoAssay, towards wash- and pump-free point-of-care diagnostics. Extending the capabilities of standard bioassays with light-dependent and reversible interaction of optogenetic switches, OptoAssays enable a bi-directional movement of assay components, only by changing the wavelength of light. Combined with smartphones, OptoAssays obviate the need for external flow control systems like pumps or valves and signal readout devices.

bioengineering↗

bioRxiv2020

Progressive changes in hippocampal stem cell properties ensure lifelong neurogenesis

Neural stem cell numbers fall rapidly in the hippocampus of juvenile mice but stabilise during adulthood, ensuring lifelong hippocampal neurogenesis. We show that this reduction in stem cell depletion rate is the result of multiple coordinated changes in stem cell behaviour. In particular, while active neural stem cells divide only once or twice before differentiating rapidly in juveniles, they increasingly return to a resting state of shallow quiescence and progress through additional self-renewing divisions in adulthood. Single-cell transcriptomic, mathematical modelling and label-retention analyses indicate that resting cells have a higher activation rate and greater contribution to neurogenesis than dormant cells, which have not left quiescence. These progressive changes in stem cell behaviour result from reduced expression of the pro-activation protein ASCL1 due to increased post-translational degradation. These mechanisms help reconcile current contradictory models of hippocampal NSC dynamics and may contribute to the different rates of decline of hippocampal neurogenesis in mammalian species including humans.

developmental biology↗

bioRxiv2019

Global ribosome profiling reveals that mutant huntingtin stalls ribosomes and represses protein synthesis independent of fragile X mental retardation protein

The regulators that stall ribosome translocation are poorly understood. We find that polyglutamine-expanded mutant Huntingtin (mHtt), the Huntingtons disease (HD) causing protein, promotes ribosome stalling and physiologically suppresses protein synthesis. A comprehensive, genome-wide analysis of ribosome footprint profiling (Ribo-Seq) revealed widespread ribosome stalling on mRNA transcripts and a shift in the distribution of ribosomes toward the 5 end, with single-codon unique pauses on selected mRNAs in HD cells. In Ribo-Seq, we found fragile X mental retardation protein (FMRP), a known regulator of ribosome stalling, translationally upregulated and it co-immunoprecipitated with mHtt in HD cells and postmortem brain. Depletion of FMRP gene, Fmr1, however, did not affect the mHtt-mediated suppression of protein synthesis or ribosome stalling in HD cells. Consistent with this, heterozygous deletion of Fmr1 in Q175FDN-Het mouse model, Q175FDN-Het; Fmr1+/-, showed no discernable phenotype, but a subtle deficit in motor skill learning. On the other hand, depletion of mHtt, which binds directly to ribosomes in an RNase-sensitive manner, enhanced global protein synthesis, increased ribosome translocation and decreased stalling. This mechanistic knowledge advances our understanding of the inhibitory role of mHtt in ribosome translocation and may lead to novel target(s) identification and therapeutic approaches that modulate ribosome stalling in HD.\n\nOne Sentence SummaryHuntingtons disease (HD) protein, mHtt, binds to ribosomes and affects their translocation and promotes stalling independent of the fragile X mental retardation protein.

neuroscience↗

bioRxiv2019

Mouse navigation strategies for odor source localization

Navigating an odor landscape is a critical behavior for the survival of many species, including mice. One ethologically relevant mouse behavior is locating food using odor concentration gradients. To model this behavior, we use a naturalistic open field odor-based spot-finding task, examining navigation strategies as mice search for and approach an odor source. Mice were trained to navigate to odor sources paired with food reward. We detected behavioral changes consistent with localization of the odor source when mice were [~]10cm away from the source. These behaviors included both orientation towards the source and increased exploration time. We found that the amplitude of casting, lateral back and forth head movement, increased exponentially with proximity to the source. We then created concentration-dependent models to simulate mouse behavior, which provided evidence for a serial-sniffing strategy (sampling concentration, moving in space, then sampling again) and a stereo-sniffing strategy (inter-nostril comparison of concentration in a single sniff). Together, these results elucidate key components of behavioral strategies for odor-based navigation. SUMMARY STATEMENTUse of a naturalistic odor-source localizing task uncovers key strategies underlying successful mouse navigation. Concentration-dependent models successfully recapitulate mouse behavior and reveal important behavioral components.

neuroscience↗

bioRxiv2018

Id4 eliminates the pro-activation factor Ascl1 to maintain quiescence of adult hippocampal stem cells

Quiescence is essential for the long-term maintenance of adult stem cells and tissue homeostasis. However, how stem cells maintain quiescence is still poorly understood. Here we show that stem cells in the dentate gyrus of the adult hippocampus actively transcribe the pro-activation factor Ascl1 regardless of their activation state. We found that the inhibitor of DNA binding protein Id4 suppresses Ascl1 activity in neural stem cell cultures. Id4 sequesters Ascl1 heterodimerisation partner E47, promoting Ascl1 protein degradation and neural stem cell quiescence. Accordingly, elimination of Id4 from stem cells in the adult hippocampus results in abnormal accumulation of Ascl1 protein and premature stem cell activation. We also found that multiple signalling pathways converge on the regulation of Id4 to reduce the activity of hippocampal stem cells. Id4 therefore maintains quiescence of adult neural stem cells, in sharp contrast with its role of promoting the proliferation of embryonic neural progenitors.

cell biology↗