Biology subjects

Rao, M.

Publications and source records attributed to Rao, M..

At least 19 recordsLinked to original sources

bioRxiv2026

Revisiting the evolution of population stability due to selection for rapid development and early reproduction in Drosophila: the role of generation length

The ubiquity of stable populations in nature generated considerable interest in how population stability might evolve, especially after the realization that higher per capita population growth rates typically yield unstable dynamics. Yet, most empirical and theoretical treatments implicitly assume that population dynamics and stability are invariant to generation length, an assumption that remains largely untested. Theory suggested that population stability could evolve as a correlated response to life-history evolution, which was first experimentally demonstrated using D. melanogaster populations selected for rapid development and early reproduction (FEJs). Constancy stability of FEJs evolved to be higher than their ancestral controls (JBs), likely due to correlated reductions in fecundity and pre-adult survivorship. However, that study assessed stability on a 21-day generation length (matching the JBs), resulting in a considerable mismatch with the generation length of FEJs (10 days). This raises a broader question of whether the observed differences in stability reflect evolved life-history changes or are an artifact of the generation length at which the populations were assayed. To address this, we assessed the stability of FEJs, JBs, and relaxed-selection populations derived from the FEJs (CRFs and FRFs) across two generation lengths (12 and 18 days), tracking 320 small populations for 27 generations. Contrary to the earlier findings based on a 21-day generation length study, FEJs did not differ in constancy from JBs when assayed at a shorter generation length. Thus, even a modest difference in life-cycle length can significantly influence population stability, thereby underscoring the need to account for generation length when comparing stability across populations. Interestingly, constancy and persistence stability of selection regimes evolved in opposite directions, highlighting the need to assess stability along multiple axes. We discuss these results using an empirical framework, emphasizing its utility over simple population growth models for a richer understanding of population dynamics and stability.

ecology↗

bioRxiv2026

Neurokinin 1 receptor blockade is associated with increased survival of patients with C. difficile infection

Clostridioides difficile is a major cause of healthcare associated infections. C. difficile infection (CDI) is a toxin-mediated disease driven by the secretion of two large protein toxins, Toxin A (TcdA) and Toxin B (TcdB). TcdA and TcdB cause neurogenic inflammation that can contribute to intestinal inflammation in rat and mouse models. Substance P (SP), a potent vasoactive neuropeptide, is a major contributor to C. difficile toxin induced inflammation in animal models. SP acts on multiple receptors including the high affinity receptor NK1-R, and lower affinity receptors (Mrgprb2 and NK2-R). Through in vivo mouse infection models, we confirmed the effects of SP in hypervirulent C. difficile are largely mediated by the neurokinin-1 receptor (NK1-R), the high affinity receptor for SP. Through genetic mice that lack mast cells (cKitW-sh) we determined that mast cells which respond to SP in certain kinds of neurogenic inflammation appear dispensable for inflammation caused by C. difficile infection. We explored the role of NK1-R antagonists in a retrospective study of a large clinical cohort. We determined that, after propensity matching, NK1-R antagonists were associated with a significant survival benefit and that patients treated with NK1-R antagonists showed evidence of reduced vascular inflammation (increased serum albumin). Together these data suggest blocking SP activity through antagonism of NK1-R with small molecule inhibitors may be a useful strategy for adjunctive treatment during C. difficile infection.

microbiology↗

bioRxiv2026

Colitis-induced visceral pain recruits central neurotensin neurons that modulate colonic sensitivity

Inflammatory bowel disease produces debilitating visceral pain that remains a major clinical challenge. Notably, many patients experience persistent pain even after the inflammation resolves, indicating a sustained sensitization of central neural circuits that drives enduring pain. The brainstem parabrachial nucleus integrates interoceptive signals from the gastrointestinal tract to elicit both pain perception and affective responses. Using activity-dependent mapping and an RNAscope assay, we identified a neurotensin (NT)-expressing neuronal population in the lateral PBN (PBNL) that is selectively activated during dextran sulfate sodium-induced colitis. In vivo neural activity recordings demonstrate that PBNL NT neurons encode colon-derived nociceptive signals in an intensity-dependent manner. Silencing these neurons attenuates colonic reflexes evoked by luminal distension and normalizes aberrant gastrointestinal transit and nociceptive licking behavior in colitic mice. Pharmacological blockade of NT signaling alleviates colitis-associated hypersensitivity. These findings identify a central neural population that encodes visceral inflammation and regulates peripheral organ function, and pinpoints neurotensin as a promising therapeutic target to treat colitis-induced visceral pain.

neuroscience↗

bioRxiv2025

Diverse ancestral myosin motors generate and segregate distinct types of nanocluster-rich domains at the plasma membrane

Molecular organization of the plasma membrane (PM) at nano and micron scales is critical for its function in all living cells. This emerges not only from the self-assembly of lipids and proteins but also from active forces originating in the underlying cytoskeletal cortex. These forces drive membrane molecules into non-equilibrium steady state patterns such as nanoclusters. However, the molecular agents connecting membrane organization with cytoskeletal dynamics and stresses have remained unknown. Here we show that two classes of ubiquitous ancestral non-muscle myosins are deployed for the organization of different types of membrane components. Inner-leaflet localized Class I myosins link outer-leaflet GPI-anchored molecules to juxta-membrane actin-filaments, whereas the more cortically-localized Class II myosins operate on transmembrane proteins endowed with actin-binding capacity. Consistent with an active Flory Huggins theory for phase separation, these observations show that the distinct motor-driven membrane molecules generate spatially segregated mesoscale domains, enriched in nanoclusters derived from different myosin classes. Moreover, chemically reversible post-translational modifications such as palmitoylation enable concatenation of these domains by enhancing affinity of the membrane domain constituents for each other. We anticipate that the segregation potential of the ATP-fueled cell membrane is made available for the crucial purpose of modulating information transduction because it can be regulated in space and time during the construction of signaling cascades, underpinning functional plasma membrane organization.

cell biology↗

bioRxiv2025

Active flows drive clustering and sorting of membrane components with differential affinity to dynamic actin cytoskeleton

Several cell membrane proteins, including signalling receptors and cell adhesion receptors, bind to contractile cortical F-actin at the cytoplasmic leaflet. Interaction with contractile actomyosin and associated actin flows drives these proteins into nanoscale clusters and mesoscopic assemblies of physiological relevance. In the context of diverse actin-binding membrane proteins, we ask how a specific composition of the local cluster/assembly may be achieved. Using in vitro reconstitution together with kinetic Monte Carlo simulations our studies reveal that an interplay between differential actin-binding affinity, protein-protein interactions and actomyosin remodelling leads to specific molecular patterning within a cluster and sorting between clusters. We show that in the lamellipodia of spreading cells in vivo, actin flows also result in the sorting of high and low-affinity actin-binders. This affinity-based sorting mechanism provides an attractive means for locally controlling cell membrane composition via engagement with the active cortical meshwork beneath.

cell biology↗

bioRxiv2025

Stepwise Ligand Capture Primes PKR for Activation and RNA Discrimination

Protein Kinase R (PKR) triggers the innate immune response upon detecting double-stranded RNAs (dsRNAs). Its kinase activity is controlled by two dsRNA-binding domains (dsRBDs), yet how these dsRBDs operate during RNA ligand recognition and downstream signaling remains unresolved. Here, we uncover an unexpected interplay between the dsRBDs that orchestrates a two-step ligand sampling, ensuring accurate and efficient PKR activation. dsRBD1 surveys all RNA duplexes through one-dimensional diffusion but dissociates within milliseconds to minimize background signaling, while dsRBD2-RNA binding plays a key role in fostering kinase-kinase interactions. Upon encountering foreign dsRNAs, dsRBD2 arrests the diffusive dsRBD1, thereby establishing a scaffold essential for kinase dimerization and phosphorylation. By contrast, prevalent bulges and large internal loops in self-RNA duplexes obstruct dsRBD2 from capturing dsRBD1, creating a steeply elevated energy landscape that enables PKR to discriminate foreign RNAs from abundant self-RNAs, thus evolving a delicate strategy to achieve both high selectivity and robust signaling.

biophysics↗

bioRxiv2025

Force patterning drives cell flows and 3D spatial order in auditory epithelia

During development, coordinated cell behavior drives the morphogenesis of epithelia into intricate structures essential for their physiological functions. How this coordination is achieved in epithelia composed of multiple cell types remains unclear. We study development of the avian auditory epithelium comprising sensory hair cells (HCs) and non-sensory supporting cells (SCs). Initially, HCs and SCs are arranged into mosaics by Notch-Delta signaling. During development, HCs partially extrude from the epithelium, establish a ten-fold gradient in apical surface area across the tissue, and intercalate with SCs to form near-hexagonal order. Using a combination of experiments and a 3D-vertex model, we show that an increase of contractility at the apical junctions between SCs compared to those between HCs and SCs drives spatial order within the epithelial plane and along the apical-basal axis. A faster increase of HC apical area at one end of the epithelium than the other leads to opposite fluxes of HCs and SCs and establishes the observed gradients in apical surface area and density of HCs along the auditory epithelium while maintaining a uniform degree of hexagonal order throughout. Our findings reveal that patterned junctional contractility can spatially coordinate cell behavior across both the plane and depth of a mixed epithelium, providing a general mechanism for generating complex three-dimensional tissue architectures during organogenesis.

developmental biology↗

bioRxiv2025

Fitness effects of adult crowding in Drosophila: more than just overall density

Density-dependent selection has been widely studied in D. melanogaster in the context of larval crowding, revealing its impact on several life-history traits. However, the effects of adult crowding in Drosophila have not been studied in similar detail. Earlier studies on adult crowding have primarily used large flies (reared at low larval density). These gave rise to the notion that adult crowding negatively affects key fitness components such as mortality and fecundity. Earlier work from our lab showed that body size significantly alters how flies respond to a relatively short period of adult crowding. Large flies show increased mortality and decreased fecundity with increased adult density. In contrast, small flies (reared at high larval density) tolerate adult crowding better, showing increased fecundity with increased adult density. Here, we extend this line of work by investigating how air volume in a culture vial can influence the effects of adult crowding. We manipulated air volume by altering the vial diameter (thereby also the food surface area), or the height of the air column. Flies of different body sizes were generated by rearing them at low or high larval densities. We find that the surface area of food available to the adults plays a greater role in shaping the outcome of adult crowding than the height of the air column. Large flies displayed context-dependent responses to adult crowding that were driven by the surface area of food provided. Small flies consistently responded positively to adult crowding in all conditions, with low mortality and increased fecundity at high adult density. Our findings highlight the importance of considering the body size, absolute density and the food surface area available to the flies and their nuanced interactions while exploring the effects of adult crowding, and thus paves the way for a detailed examination of other factors that impact adult crowding in addition to just the overall density.

ecology↗

bioRxiv2025

Bigger is not always better: size-dependent fitness effects of adult crowding in Drosophila melanogaster

Density-dependent selection is an important factor shaping the evolution of life histories. In holometabolous insects, crowding in the larval and adult stages can have very different effects on key fitness components. While the nuanced effects of density-dependent selection through larval crowding in Drosophila melanogaster have been extensively studied for various life history traits, very few studies have investigated the effects of adult crowding in Drosophila. Moreover, these few studies were mostly conducted on large flies, derived from low larval density cultures, and typically treated the overall density of flies per culture container as an index of the strength of adult crowding. We hypothesized that the size of the adults should shape the impact of adult crowding, with small individuals experiencing less stress than large individuals when crowded. Consequently, the adverse fitness effects usually associated with adult crowding may not be observed for small individuals. We tested this hypothesis by subjecting flies of different sizes - regular-sized flies, and small flies derived via larval crowding or selection for rapid development to adulthood - to an episode of adult crowding and examining their mortality and fecundity. Thus, we explored the interactive effects between larval and adult crowding on key fitness components. Small body size enabled flies to handle adult crowding better, with significantly lower mortality under crowded conditions when compared to flies of large body size. Moreover, small flies showed a consistent pattern of increased fecundity upon adult crowding. This positive impact on fecundity was not observed when larger flies were crowded. It is clear from our study that the effects of adult crowding can be very nuanced and body size-specific, even to the extent of having a net beneficial effect on fitness components, contrary to previous belief.

ecology↗

bioRxiv2025

Coordinated IFN-γ/TNF Axis Drives Selective Loss of Activated Enteric Glia in Inflammatory Bowel Diseases

BackgroundEnteric glial cells (EGC) play a crucial role in maintaining gut homeostasis, but their dysregulation in inflammatory bowel diseases (IBD) remains poorly understood. Emerging preclinical data suggests activated EGC have beneficial roles in controlling gut pathophysiology. ObjectiveUnderstanding EGC activation and adaptation during experimental and clinical IBD. DesignWe provide the first highly integrated approach to identify EGC activation signature in IBD. Profiling 390 samples from IBD patients via bulk and single-nucleus (sn) transcriptomics and replicate the findings on publicly available bulk and single-cell (sc) datasets from 1160 patients and 19,000 single EGC. Preclinical modelling of Th1/Th17 inflammation, reporter-assisted EGC sorting, analysis of regulated cell death, and Casp8 ablation in EGC was performed ResultsWe identified novel IBD type and sampling associated EGC activation signature. Specific EGC activation markers were shared in biopsies and resection specimens, and were divergent between Crohns disease and Ulcerative colitis. Preclinical modelling of intestinal inflammation identified combinatorial TNF and IFN-{gamma}-driven activation of EGC, associated with elevated necroptosis, and negatively impacting gut motility. Genetic-reporter-enabled sorting and downstream analyses confirmed TNF and IFN-{gamma}-driven EGC necroptosis, potentiated by Casp8 deficiency. Furthermore, snRNA-Seq from IBD patient samples confirmed elevated cell death signature in activated but not in rare neuroglia progenitor-like cluster. ConclusionOur findings identify IBD type-associated activated EGC markers involved in immune and epithelial homeoastasis. We uncover necroptosis of activated EGCs as a constituent of intestinal inflammation. Advancing our understanding of activated EGC survival is pivotal in elucidating their complex roles in maintaining gut immune-epithelial homeostasis. What is already known on this topicActivated EGC have emerged as important contributors in maintaining epithelial, immune and neuronal homeostasis. Increasing evidence from mouse studies points to the role of activated EGC in epithelial regeneration, tolerogenic T-cell activation, relaying psychological stress to the enteric nervous system, post-injury neurogenesis, and helminth clearance. Nevertheless, no consensus has emerged on what might define activated EGC in the context of IBD and how EGC turnover is affected in gut inflammation, limiting translation of their disease associated roles. What this study addsBy combining bulk with single cell and single nucleus transcriptomes from IBD patients we identified new IBD type- and location-associated EGC activation signatures. Some of these are conserved with mouse EGC in gut inflammation models. We identified osteopontin an immunomodulator and Wnt6 an epithelial morphogen elevated in IBD EGC. We also identified IBD-associated EGC cell clusters, which display higher expression of cell death pathway transcripts. To investigate EGC turnover, we utilized preclinical models and found rapid EGC activation upon Th1/Th17 inflammation. This was associated with elevated EGC activation and caspase-independent necroptotic cell death. Ex vivo experiments showed a combinatorial requirement of IFN-{gamma} and TNF in mediating EGC necroptosis. Our findings were replicated on multiple publicly available sc-RNA sequencing datasets from IBD patients. How this study might affect research, practice or policyExpanding on the available repertoire of EGC activation markers in IBD, both shared and unique to sampling procedure, disease type, and location will provide researchers with tools to identify EGC homeostasis during IBD. Moreover, the nature of the identified markers will stimulate research into specific EGC pathways triggered in inflammation. Adding to this, the rapid induction in pathological death of activated but not naive EGC upon IFN-{gamma} and TNF stimulation will shed light on EGC adaptation and turnover. Our identification of markers of activated EGC with immuno-modulatory and epithelial-regenerative properties, including osteopontin and wingless family of morphogenes will stimulate further research in EGC-immune and EGC-epithelial communication in the context of IBD.

neuroscience↗

bioRxiv2025

Excitability and travelling waves in renewable active matter

Activity and renewability are distinctive features of living matter, and constitute a new class of materials that we term renewable active matter. A striking example is the cell cytoskeleton, where myosin filaments bind to the actin meshwork, apply contractile stresses and undergo continual stress/strain dependent turnover, thus acting as both force generators and sensors. As a consequence of nonreciprocity, arising from the independence of action and response, such living matter exhibits unusual mechanical properties like, segregation without attraction, fragility and force chains. Here we show that the interplay between activity and turnover gives rise to mechanical excitability in the form of travelling waves and pulses, and spatiotemporal chaos. We provide a systematic study of the nucleation, movement and shape of the travelling pulse, and present a boundary layer analysis to establish the existence of homoclinic orbits. Our analytical results are supported by detailed numerical analysis of the governing partial differential equations. This study has implications for the observed mechanical excitability in a variety of cellular contexts such as in isolated adherent cells and confluent cells within tissues.

biophysics↗

bioRxiv2025

Comprehensive cellular analysis with single-nucleus RNA-seq of archived PAXgene whole blood samples

No method has been developed for single-cell analysis of the large repositories of preserved whole blood samples stored in PAXgene Blood RNA tubes. To address this gap, two nuclei isolation techniques for single-nucleus RNA sequencing were evaluated: mechanical separation (MS), using an Acrodisc filter, and cell lysis (CL). While both methods captured nuclei from all major immune cell types, CL resulted in up to two orders of magnitude higher nuclei yields and less biased proportions of immune cells than MS. High ambient globin gene counts following CL were substantially reduced by CRISPR-guided globin gene depletion of complementary DNA, resulting in more sensitive and efficient gene detection per cell. Despite capturing only nuclear transcripts, CL-derived samples maintained similar cell-type proportions and gene expression as matched peripheral blood mononuclear cell samples, while retaining granulocytes. The CL isolation with globin depletion method enables comprehensive analysis of PAXgene whole blood samples at single-cell resolution. MOTIVATIONPAXgene Blood RNA Tubes are commonly used for blood preservation and gene expression studies due to the ease of use and stabilization of RNA. To date, transcriptomic studies using PAXgene tubes have been limited to bulk RNA profiling approaches such as RNA sequencing (RNA-seq). Here we introduce a method for recovering high-quality nuclei from frozen blood preserved in PAXgene tubes for single-nucleus RNA-seq (snRNA-seq). Using this approach, all white blood cell types - including granulocytes - are captured, thereby enabling comprehensive transcriptomic profiling of peripheral blood at single-cell resolution.

genomics↗

bioRxiv2025

A niche-dependent redox rheostat regulates epithelial stem cell fate in the distal colon

The niche environment surrounding intestinal stem cells (ISCs) varies along the length of intestine and provides key cues that regulate stem cell fate. Here, we investigated the role of cellular redox balance in colonic ISC function. We show that hypoxia and Wnt signaling synergize to restrict the reactive oxygen species (ROS) generating enzyme NADPH oxidase 1 (NOX1) to the crypt base in the distal colon. NOX1 function maintains a more oxidative cell state that licenses cell cycle entry, altering the balance of asymmetric stem cell self-renewal and directing lineage commitment. Mechanistically, cell redox state directs a self-reinforcing circuit that connects hypoxia inducible factor 1 (HIF1)-dependent signaling with regulation of the metabolic enzyme isocitrate dehydrogenase 1 (IDH1). Our studies show that cellular redox balance is a central and niche-dependent regulator of epithelial homeostasis and regeneration and provide a basis for understanding disease propensity in the distal large intestine. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=176 SRC="FIGDIR/small/634856v2_ufig1.gif" ALT="Figure 1"> View larger version (55K): org.highwire.dtl.DTLVardef@107798aorg.highwire.dtl.DTLVardef@1bc9013org.highwire.dtl.DTLVardef@96d56aorg.highwire.dtl.DTLVardef@95268d_HPS_FORMAT_FIGEXP M_FIG C_FIG HIGHLIGHTSO_LIThe balance of cycling intestinal stem cells (ISCs) versus committed epithelial cells in the uniquely hypoxic niche of the distal colon is regulated by NADPH oxidase 1 (NOX1) dependent H2O2 both at homeostasis and during regeneration. C_LIO_LIPhysiological increase in cellular H2O2 favors maintenance of glycolysis in ISCs for self-renewal through regulation of isocitrate dehydrogenase 1 activity. C_LIO_LIMaintenance of the increased cellular oxidative state stabilizes HIF1 through a re-enforcing metabolic circuit. C_LIO_LIA shift from a relatively oxidative to a reductive cell environment in distal colonic ISCs leads to decreased progression through the cell cycle and altered cell fate determination. C_LI

cell biology↗

bioRxiv2024

Human-immune-system humanized-DRAGA mice are a valuable model to study novel immunotherapies for HIV-1

Humanized (h)DRAGA mice are a promising in vivo model for investigating immunotherapies for treating HIV infections. These mice are not only susceptible to HIV infection, but they also develop functional human immune cells, including T cells and B cells as well as follicular-like structures that mimic lymphoid B cell follicles, where HIV-producing cells concentrate during infection in a manner similar to that found in humans. This study evaluated the safety, tissue targeting, and efficacy of follicular-targeting HIV-specific chimeric antigen receptor (CAR)-T cells (CAR/CXCR5-T cells) in HIV-infected hDRAGA mice. Intravenously-infused CAR/CXCR5-T cells persisted in hDRAGA mice for the duration of the study, peaking six days post-infusion. This study indicated that CAR/CXCR5-T cell treatment is safe, with 100% survival rate of treated mice and no noticeable changes in pathology. Six days after infusion, CAR/CXCR5-T cells had accumulated in the follicle-like structures, with many appearing in direct contact with HIV-producing cells. However, CAR/CXCR5-T cell treatment did not appear to reduce viral loads compared to controls, perhaps because many of the engineered CAR/CXCR5-T cells were themselves infected with HIV, with some CAR/CXCR5-T cells showing evidence of HIV virion release. Future studies will investigate whether CAR/CXCR5-T cells engineered for resistance against HIV infection are effective in reducing viral loads. This study supports the approach of using the HIV-infected hDRAGA mouse model to test cellular immunotherapies for HIV, as the model recapitulates many aspects of HIV infection in human lymphoid follicles.

immunology↗

bioRxiv2024

PTBP1 is upregulated by Zika virus infection via HIF-1alpha signal and hijacks NS1 protein to induce NS1 degradation to restrain viral replication

Zika virus (ZIKV), belonging to the Flaviviridae family, has been a severe threat to human health since the worldwide outbreak. ZIKV is capable of inducing fetal microcephaly, Guillain-Barre syndrome, and other serious neurological complications. Polypyrimidine tract-binding protein 1 (PTBP1) is a key member of the heterogeneous nuclear ribonucleoproteins (hnRNPs) family, functioning in selective mRNA splicing and gene expression regulation. Our previous study has indicated that the expression of PTBP1 increases in astrocytes upon ZIKV infection, yet the precise regulatory mechanisms underlying its role in viral replication remain elusive. In this study, we elucidated the specific pathway by which ZIKV upregulates PTBP1 expression through the activation of Hypoxia-inducible factor-1 (HIF-1) expression. Further investigation revealed that overexpression of PTBP1 effectively inhibits viral replication, whereas knockdown of PTBP1 significantly enhances viral replication. Mechanistically, using co-immunoprecipitation assays for protein interaction screening, we identified an interaction between PTBP1 and ZIKV non-structural protein NS1. Detailed studies demonstrated that PTBP1 bound and colocalized with NS1 to lead to the degradation of NS1 protein via a lysosomal pathway. Collectively, our findings unveil a novel mechanism underlying that ZIKV infection induces the expression of PTBP1 via the HIF-1 pathway, subsequently the accumulated PTBP1 binds to ZIKV NS1 protein to promote NS1 degradation, thereby effectively inhibiting viral replication. The study illustrates a distinct restricted cellular factor that regulates ZIKV replication, which provides a potential target for the control of the viral replication and pathogenesis during the ZIKV epidemic. ImportanceSince the outbreak of ZIKV infection among human in 2014, a Zika epidemic has caused Zika fever accompanied with fetal microcephaly, Guillain-Barre syndrome, and other neurological symptoms. Emerging evidence reveals that ZIKV infects astrocytes to specially induce the expression of polypyrimidine tract-binding protein 1 (PTBP1), one of hnRNPs members. However, the interplay between PTBP1 and ZIKV replication is highly concerned. Here, we uncover a distinct manner that ZIKV infection induces PTBP1 expression through the activation of hypoxia-inducible factor-1 (HIF-1) signal. Additionally, activation of HIF-1 signal hinders ZIKV replication relying on PTBP1 accumulation. Further investigations suggest that PTBP1 restrains ZIKV replication by interacting with ZIKV NS1 protein, thereby leading to the degradation of NS1 protein via a lysosomal pathway. Collectively, our findings illustrate a novel restricted cellular factor PTBP1 mediated by HIF-1 that regulates ZIKV replication, which provides a potential therapeutic target of the viral replication and pathogenesis against ZIKV pandemic.

microbiology↗

bioRxiv2024

Novel nanopore sequencing method for determining Human Papillomavirus integrations in tumors without the need for whole genome sequencing

Human papillomaviral (HPV) integrations into host human genome, a key event in cervical carcinogenesis, are currently mapped through laborious and expensive sequencing methodologies. We developed and validated a novel library preparation strategy for nanopore sequencing to generate long targeted reads with HPV and human chimeric sequences. Using this strategy, we validated known HPV integrations in HeLa (HPV18) and SiHa (HPV16) cell lines. We also mapped integration sites in five HPV+ cervical cancer patients, which were confirmed by whole genome and Sanger sequencing. Our nanopore-based method provides a precise and efficient strategy to capture HPV integrations crucial for understanding tumorigenesis.

genomics↗

bioRxiv2024

Active morphodynamics of intracellular organelles in the trafficking pathway

From the Golgi apparatus to endosomes, organelles in the endomembrane system exhibit complex and varied morphologies that are often related to their function. Such membrane-bound organelles operate far from equilibrium due to directed fluxes of smaller trafficking vesicles; the physical principles governing the emergence and maintenance of these structures have thus remained elusive. By understanding individual fission and fusion events in terms of active mechano-chemical cycles, we show how such trafficking manifests at the hydrodynamic scale, resulting not only in fluxes of material-- such as membrane area and encapsulated volume-- but also in active stresses that drive momentum transfer between an organelle and its cytosolic environment. Due to the fluid and deformable nature of the bounding membrane, this gives rise to novel physics, coupling nonequilibrium forces to organelle composition, morphology and hydrodynamic flows. We demonstrate how both stable compartment drift and ramified sac-like morphologies, each reminiscent of Golgi-cisternae, emerge naturally from the same underlying nonequilibrium dynamics of fission and fusion.

biophysics↗

bioRxiv2024

Segregation, Finite Time Elastic Singularities and Coarsening in Renewable Active Matter

Material renewability in active living systems, such as in cells and tissues, can drive the large-scale patterning of forces, with distinctive phenotypic consequences. This is especially significant in the cell cytoskeleton, where multiple species of myosin bound to actin, apply differential contractile stresses and undergo differential turnover, giving rise to patterned force channeling. Here we study the dynamical patterning of stresses that emerge in a hydrodynamic description of a renewable active actomyosin elastomer comprising two myosin species. Our analytical framework also holds for an actomyosin elastomer with a single myosin species. We find that a uniform active contractile elastomer spontaneously segregates into spinodal stress patterns, followed by a finite-time collapse into tension carrying singular structures that display self-similar scaling and caustics. Our numerical analysis carried out in 1D, shows that these singular structures move and merge, and gradually result in a slow coarsening dynamics. We discuss the implications of our findings to the emergence of stress fibers and the spatial patterning of actomyosin. Our study suggests, that with state-dependent turnover of crosslinkers and myosin, the in vivo cytoskeleton can navigate through the space of material parameters to achieve a variety of functional phenotypes.

biophysics↗