Biology subjects

Pradhan, A.

Publications and source records attributed to Pradhan, A..

At least 19 recordsLinked to original sources

bioRxiv2026

Germinal centers can persist for up to one year with declining somatic hypermutation and ongoing plasma cell output

The total duration of primary germinal center (GC) responses, and how B cell evolution changes as these responses mature, remain poorly defined. Here, longitudinal sampling of rhesus macaques immunized with HIV Envelope protein revealed that a single slow-delivery prime sustained ongoing GCs for nearly a year without additional antigen. Somatic hypermutation (SHM) accumulated throughout these prolonged responses, but its rate declined substantially over time, independent of both priming strategy and boosting. Over the same period, subdominant non-base Env specificities became increasingly represented within the GC response. Delaying boosting until after primary GC contraction increased recruitment of recalled memory B cells into the GC response. Bone marrow plasma cells were generated throughout prolonged GC maturation, with the timing of their generation modulated by booster timing. Together, these findings reveal how GCs evolve across nearly a year and how this prolonged maturation shapes the memory and plasma cell compartments that underpin long-term humoral immunity.

immunology↗

bioRxiv2026

Loss of riboflavin biosynthesis leads to accumulation of select aromatic amino acids and loss of infectivity in Mycobacterium tuberculosis

Riboflavin biosynthesis is required for in vitro survival of the human pathogen Mycobacterium tuberculosis (Mtb). However, despite the lack of a known transporter, growth can be rescued by exogenous riboflavin. The riboflavin biosynthesis pathway is also predicted essential in vivo, but whether riboflavin levels available in the host can support survival has not been directly tested. Here we constructed a set of inducible CRISPR interference (CRISPRi) knockdown and targeted gene deletion strains for known riboflavin biosynthesis genes (ribA2, ribG, ribH, ribC) as tools to characterize riboflavin requirements, uptake, and metabolite changes and to assess in vivo essentiality. We found that riboflavin, but not flavin adenine dinucleotide or flavin mononucleotide, rescued auxotrophy for all strains tested. Further, riboflavin uptake did not show strong evidence of being dependent on active or facilitated transport, supporting the mechanism of passive diffusion. Targeted metabolite profiling after removal of riboflavin from growth medium confirmed reduced riboflavin levels. While other riboflavin intermediates were not detected, significant accumulation of aromatic amino acids (Phe, Tyr) was observed across all assayed strains, as well as alteration in a vitamin B9 metabolite. Selecting the ribC knockout as a representative strain, we found that riboflavin depletion had a bacteriostatic effect as late as 3 weeks after removal. Unexpectedly, {Delta}ribC lacked infectivity in an aerosol mouse infection, suggesting that the potential to scavenge riboflavin from the host is not sufficient to survive in vivo. Overall, our results show that altered metabolism upon loss of riboflavin biosynthesis leads to compromised Mtb infectivity. IMPORTANCETuberculosis remains one of the worlds most deadly infectious diseases, underscoring the need to explore new drug targets. Riboflavin (vitamin B2) biosynthesis has emerged as a promising target because Mycobacterium tuberculosis (Mtb) depends on this pathway for survival. The riboflavin pathway also produces metabolites that modulate host mucosal-associated invariant T (MAIT) cell activity, towards understanding potential strategies for host-directed therapies. Here we found that disrupting riboflavin biosynthesis led to not only compromised survival, but also widespread changes to metabolism and loss of the ability to establish infection in an animal model. These findings improve our understanding of how Mtb adapts to metabolic stress, with implications for developing drugs that target riboflavin biosynthesis and for alterations in host immunity to be explored in future studies.

microbiology↗

bioRxiv2026

Evidence of residual Brugia malayi infection in TAS-III cleared areas of coastal Odisha: Findings from Molecular Xenomonitoring

BackgroundLymphatic filariasis (LF), caused by Wuchereria (W) bancrofti, Brugia malayi and Brugia (B) timori, remains a major public health problem known for its disfiguring and debilitating effects despite notable progress under the Global Program to Eliminate Lymphatic Filariasis (GPELF). Following recent national directives (2024) restructuring implementation units (IUs) to the block level, all TAS-cleared blocks now require re-evaluation using night blood surveys (NBS) or filarial test strip (FTS) kits. Molecular Xenomonitoring (MX) is recommended as a post-validation surveillance method for detecting active LF transmission in vectors. Therefore, an exploratory study was conducted in two coastal districts of Odisha, namely Jagatsinghpur and Puri, which cleared TAS-III, to investigate the presence of B. malayi and W. bancrofti infections in filaria-transmitting vectors. Methodology/Principal FindingsAdult female mosquitoes were collected from three villages across Jagatsinghpur and Puri districts during March-April 2025. Species were identified morphologically, segregated and pooled. The pooled samples were screened for the presence of filarial DNA using species-specific PCR assays. Of 1,518 collected adult female mosquitoes, 22.6% were Culex quinquefasciatus, 18.3% were Mansonia (Mn) annulifera, and 4.3% were Mansonia uniformis. Among 33 pools screened, six pools were positive for B. malayi DNA (18.18% pool positivity; infection rate 2.88%, 95% CI: 1.23-5.74), in Mn. annulifera, whereas W. bancrofti was not detected. Conclusions/SignificanceThe study provides the first molecular confirmation of B. malayi infection in Mn. annulifera, indicating a persistent Brugian transmission in Odisha even after the implementation of mass drug administration. The Study highlights MX as a sensitive, non-invasive surveillance tool for detecting residual infection in post-MDA and post-TAS settings. The study underscores the need for a standardized MX protocol and integration with entomological monitoring to sustain national LF elimination targets by 2027. Author SummaryLymphatic filariasis is a mosquito-borne disease that can cause severe, disfiguring swelling of the limbs and other lasting disabilities, and it remains a serious public health problem in India. National programmes in India are actively working to eliminate it by giving preventive medicines to communities, conducting surveys to confirm that transmission has ceased, and once an area passes, this treatment is withdrawn. However, it is not always clear whether the parasite has truly disappeared or is still lingering at very low levels. In this study, we searched for the parasite directly inside mosquitoes, an approach that does not require collecting blood from people. We sampled mosquitoes from two coastal districts of Odisha, India, that had already passed the required surveys and stopped treatment. We found the parasite Brugia malayi in Mansonia mosquitoes, the first time this has been shown using this molecular method in the region, although the more common filarial parasite was not detected. Our findings show that transmission can smoulder on even after an area is judged free of disease. Because India has no available rapid field test for this particular parasite, we argue that examining mosquitoes should become a routine safeguard for the countrys elimination effort.

zoology↗

bioRxiv2026

Chronic postnatal chemogenetic activation of forebrain excitatory neurons modulates adult glial function and metabolism in male mice

Early adversity increases vulnerability for adult psychopathology. Across multiple pre-clinical models of early adversity, there are reports of glial dysfunction and disrupted amino acid neurotransmission, along with maladaptive behavioral responses in adulthood. Disrupted G-protein coupled receptor signaling is known to phenocopy specific consequences of early life adversity. Enhanced Gq signaling in the forebrain excitatory neurons in early postnatal life programs anxio-depressive behaviors in adulthood, accompanied by altered neuronal glutamate and GABA metabolism in mouse models. We hypothesized that enhancing Gq signaling in forebrain excitatory neurons in early postnatal life may also impact glial function in adulthood. Our results show that postnatal hM3Dq-mediated chemogenetic activation of CaMKII-positive forebrain excitatory neurons not only increases anxiety-like behavior, but also evokes bidirectional transcriptional regulation of multiple glia-associated genes in the neocortex and hippocampi. While Gfap, Aldh1l1, S100{beta}, Eaat1, Eaat2 and Eaat3, mRNA levels were reduced in the neocortex, they were enhanced in the hippocampus, and a similar pattern was noted for GFAP protein levels. Transient, postnatal chemogenetic activation of CaMKII-positive neurons did not alter astrocyte cell density in both the neocortex and the hippocampus. Using (1H-(13C)) NMR spectroscopy, we observed a significant decline in astrocyte-specific glutamate and GABA neurotransmitter turnover, and a reduction in astrocyte metabolic flux within the neocortex and the hippocampus in adulthood in animals with a history of postnatal chemogenetic activation of forebrain excitatory neurons. Our findings indicate that chemogenetically driving Gq signaling transiently during the postnatal window in forebrain excitatory neurons results in persistent changes well into adulthood, with enhanced anxiety-like behaviors and disrupted glial function and metabolism, phenocopying specific changes in glial function noted following early adversity.

neuroscience↗

bioRxiv2026

Nanoparticle-delivered resiquimod induces brain tumor regression in medulloblastoma and diffuse midline glioma models by interrupting paracrine growth support and activating myeloid immune signaling and phagocytosis

In pediatric brain tumors medulloblastoma (MB) and diffuse midline glioma (DMG), tumor-associated myeloid cells (TAMs) support malignant progression by secreting paracrine growth factors and suppressing local immune function. We studied the potential for reversing this cancer-supportive phenotype by stimulating TAM pathogen receptors using ResiPOx, a brain-permeant, polyoxazoline nanoparticle formulation of the TLR7/8 agonist resiquimod. ResiPOx showed blood-brain barrier penetration and anti-tumor efficacy, extending progression-free survival (PFS) in mice with MB and DMG. Integrated cellular and molecular analysis including scRNA-seq showed that ResiPOx expanded TAM populations and reprogrammed TAMs toward anti-tumoral states, blocking paracrine IGF1 signaling and inducing local cytokine signaling and phagocytosis of tumor cells. In rhesus macaques, systemic ResiPOx was well tolerated and induced brain transcriptional patterns that resembled ResiPOx responses in DMG and MB mouse models, indicating effects in non-human primates that highlight translational potential. Our data show that ResiPOx reshapes the brain tumor microenvironment to inhibit tumor growth. As a systemically administered, brain penetrant immunomodulator, ResiPOx is able to reach multifocal and unresectable brain tumors, including MB and DMG.

cancer biology↗

bioRxiv2026

FKS1/2-variant independent mechanisms underlying the emergence of resistance in echinocandin-refractory Candida auris infections

The emerging fungus Candida auris is a drug resistant global public health threat and WHO critical priority pathogen. Recommended first-line invasive candidiasis treatment is echinocandin monotherapy, but C. auris can develop on-treatment resistance via FKS1/2 gene mutations and additional, previously unexplained mechanisms. To better understand echinocandin failure in C. auris, we sequenced the genomes of echinocandin refractory FKS1/2 wild-type C. auris serial isolates from two critically unwell patients in London, UK. Population analysis profiling revealed echinocandin heteroresistance, and in vitro culture of clinical isolates at supra-MIC concentrations of anidulafungin (8 g/ml) exhibited morphotypic heterogeneity. Small colony variants (SCVs) and large colony variants (LCVs) showed elevated MICs with polyploidy (to 4n and above) alongside adaptive changes in cell wall {beta}-1,3-glucan content. LCVs contained significantly more mutations in calcineurin-related stress tolerance pathway gene CRZ1 compared to clinical parents and SCVs, associated with further increases in MIC. These findings indicate progressive step-wise accrual of adaptation to echinocandins, including genomic instability, alterations in stress tolerance pathways, and cell wall remodeling, paving the way for resistance emergence. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=124 SRC="FIGDIR/small/700071v1_ufig1.gif" ALT="Figure 1"> View larger version (43K): org.highwire.dtl.DTLVardef@14460b7org.highwire.dtl.DTLVardef@29a598org.highwire.dtl.DTLVardef@36d187org.highwire.dtl.DTLVardef@f62c8b_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2025

Loss of MGST1 during fibroblast differentiation enhances vulnerability to oxidative stress in human heart failure

BackgroundOxidative stress (OS) resulting from an imbalance between reactive oxygen species (ROS) production and antioxidant defences is a major mechanism exacerbating HF, involving activation of cardiac fibroblasts (FB) and fibrosis. In addition to reducing ROS production and/or scavenging, boosting cellular anti-oxidant capacity is a potential strategy, with FB an interesting target. MethodsWe interrogated single-nucleus RNA sequencing (snRNA-seq) data from human failing and non-failing hearts to identify OS modulating genes. Differential gene expression analysis in FB and comparison with other cell types was used for identification of candidate genes. The functional role of the identified candidate was studied in primary isolated human FB in culture, using knock-down strategies and phenotype manipulation using TGF-{beta}1. ResultsAcross the different cardiac cell types, FB showed the greatest enrichment for OS-modulating genes downregulated in HF. Of these genes, the microsomal glutathione S-transferase 1 (MGST1), was exclusively expressed and downregulated in FB, inversely correlating with elevated ROS levels in HF tissue. TGF-{beta}1 treatment of non-HF FB reduced MGST1 expression. MGST1 knockdown in non-HF FB raised expression of periostin, but not of collagen. ROS production and susceptibility to oxidative damage and lipid peroxidation were also increased. Downregulation of ferroptosis-suppressing and iron-handling genes inversely correlated with MGST1 expression. ConclusionLoss of MGST1 in HF is unique to FB, linked to FB activation. It impairs FB antioxidant capacity, exacerbating oxidative stress, and reduces resistance to ferroptosis. Through these mechanisms, loss of FB MGST1 induces a deleterious positive feedback on cardiac remodelling in human HF.

cell biology↗

bioRxiv2025

Fusion of Complement Fragment C3d Enhances Germinal Center Responses to HIV-1 Envelope Glycoproteins

Eliciting sustained germinal center (GC) responses is critical for the development of an effective HIV-1 vaccine, yet HIV-1 envelope glycoprotein (Env) immunogens often fail to elicit GC responses required for the maturation of cognate B cells that secrete broadly neutralizing antibodies (bNAbs). Effective antigen recognition is important for initial B cell priming, activation, and GC engagement. Since complement opsonization contributes to antigen recognition, we investigated whether C3d fusion could enhance the GC response of the stabilized HIV-1 Env immunogen based on a consensus sequence (ConM Env). Our results demonstrate that ConM Env-C3d induced potent HIV-specific B cell activation in vitro compared to ConM Env alone. We also observed that the C3d fusion enhanced antigen presentation by human tonsil-derived follicular dendritic cells (FDCs) to HIV-specific B cell lines. Moreover, mouse immunization studies combining ConM Env-C3d with the AddaS03 adjuvant revealed significantly enhanced early GC formation and prolonged antigen display and retention on FDCs for up to 56 days, highlighting improved antigen persistence within GCs. These immunological enhancements, including a more focused early antibody response, correlated with improved virus neutralization. Additionally, we observed sex-based differences in immune responses, with female mice showing stronger antibody responses and enhanced antigen retention compared to males. These findings suggest that C3d fusion can enhance GC engagement and improve the immunogenicity of HIV-1 vaccines.

immunology↗

bioRxiv2025

Early onset of Ca2+ waves and synchronization in multicellular clusters facilitate focal arrhythmogenesis in human heart failure

BackgroundSpontaneous Ca2+ release events and waves are frequent in isolated ventricular cardiomyocytes from failing hearts (HF) and are proposed to initiate arrhythmias in the intact heart. However, evidence supporting whether single-cell Ca2+ waves trigger tissue-wide depolarization in the intact heart is scarce, particularly in human HF. We characterized Ca2+ waves at single-cell resolution within the multicellular network of the intact heart and identified propagating dynamics and mechanisms facilitating arrhythmogenesis at tissue level. MethodsLiving myocardial slices (LMS) from HF and non-HF human hearts were prepared from left ventricular tissue and paced at 2 Hz under adrenergic stimulation. Ca2+ transients and waves were recorded by wide-field imaging of Fluo-8. Ca2+ waves in relation to single-cell structures within each LMS were identified using custom algorithms. Computational modelling assessed whether experimentally observed HF Ca2+ waves dynamics can lead to focal excitation in tissue models. ResultsFollowing pacing, early onset Ca2+ waves, initiating within the first 2 seconds, were more frequent in HF compared to non-HF, and HF cardiomyocytes had more foci, where Ca2+ waves originate, than non-HF. Spatial mapping showed that early onset waves in HF occurred frequently in clusters of neighboring cells. Although early onset Ca2+ waves propagated similar distances in HF and non-HF cardiomyocytes, they more frequently crossed cell boundaries in HF. Particularly, HF LMS exhibited more side-to-side Ca2+ propagation, correlating with increased connexin 43 distribution to lateral membranes. Furthermore, HF LMS exhibited more local and global triggered Ca2+ activities compared to non-HF LMS, correlating with local tissue depolarization. Simulations of HF Ca2+ wave dynamics in remodeled tissue demonstrated a greater capacity to elicit focal excitation. ConclusionsIn human HF, a higher incidence of early onset Ca2+ waves combines with altered intercellular connectivity to create synchrony in clusters of nearby cells that can overcome the current sink, thereby increasing arrhythmia susceptibility. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=70 SRC="FIGDIR/small/651991v1_ufig1.gif" ALT="Figure 1"> View larger version (25K): org.highwire.dtl.DTLVardef@12582forg.highwire.dtl.DTLVardef@5b9893org.highwire.dtl.DTLVardef@17de348org.highwire.dtl.DTLVardef@1d4c420_HPS_FORMAT_FIGEXP M_FIG C_FIG

physiology↗

bioRxiv2025

CD4+ Mucosal-associated Invariant T (MAIT) cells express highly diverse T cell receptors

Mucosal-associated invariant T cells are highly conserved innate-like T cells in mammals recognized for their high baseline frequency in human blood and cytotoxic effector functions during infectious diseases, autoimmunity, and cancer. While the majority of these cells express a conserved CD8{beta}+ TRAV1-2 T cell receptor recognizing microbially-derived Vitamin B2 intermediates presented by the evolutionarily conserved major histocompatibility complex I-related molecule, MR1, there is an emerging appreciation for diverse subsets that may be selected for in humans with distinct functions, including subpopulations that co-express CD4. Prior work has not examined T cell receptor (TCR) heterogeneity in CD4+ MAIT cells, largely due to bias of identifying human MAIT cells as CD8+ TRAV1-2+ cells. In this study, we adopted an unbiased single-cell TCR-sequencing approach of total MR1-5-OP-RU-tetramer-reactive T cells and discovered that CD4+ MAIT cells express highly diverse TRAV1-2 negative TCRs. To specifically characterize this TCR repertoire, we analyzed VDJ sequences of single MR1-5-OP-RU tetramer+ MAIT cells across two datasets and identified distinct TCR usage among CD4+ MAIT cells including TRAV21, TRAV8 (TRAV8-1, TRAV8-2, TRAV8-3), and TRAV12 families (TRAV12-2, TRAV12-3), as well as more variable J chain and CDR3 sequences. Non-TRAV1-2 MAIT cell TCRs were also enriched after in vitro expansion, including with Mycobacterial tuberculosis. These results indicate that mature human CD4+ MAIT cells adopt distinct TCR usage from the canonical TRAV1-2+ CD8+ subset and suggest that alternative MR1 ligands in addition to riboflavin intermediates may select them.

genomics↗

bioRxiv2025

Vaccination with mRNA-encoded membrane-bound HIV Envelope trimer induces neutralizing antibodies in animal models

A protective vaccine against HIV will likely need to induce broadly neutralizing antibodies (bnAbs) that engage relatively conserved epitopes on the HIV envelope glycoprotein (Env) trimer. Nearly all vaccine strategies to induce bnAbs require the use of relatively complex immunization regimens involving a series of different immunogens, most of which are Env trimers. Producing protein-based clinical material to evaluate such relatively complex regimens in humans presents major challenges in cost and time. Furthermore, immunization with HIV trimers as soluble proteins induces strong non-neutralizing responses to the trimer base, which is normally occluded on the virion. These base responses could potentially detract from the induction of nAbs and the eventual induction of bnAbs. mRNA vaccine platforms offer potential advantages over protein delivery for HIV vaccine development, including increased production speed, reduced cost, and the ability to deliver membrane-bound trimers that might facilitate improved immuno-focusing to non-base epitopes. We report the design of mRNA-delivered soluble and membrane-bound forms of a stabilized native-like Env trimer (BG505 MD39.3), initial immunogenicity evaluation in rabbits that triggered clinical evaluation, and more comprehensive evaluation of B cell, T cell, and antibody responses in non-human primates. mRNA-encoded membrane-bound Env immunization elicited reduced off-target base-directed Env responses and stronger neutralizing antibody responses, compared with mRNA-encoded soluble Env. Overall, mRNA delivery of membrane-bound Env appears promising for enhancing B cell responses to subdominant epitopes and facilitating rapid translation to clinical testing, which should assist HIV vaccine development. One Sentence SummaryHIV envelope trimer mRNA enables membrane-bound expression and represents a functional immunogen in pre-clinical mammalian models.

immunology↗

bioRxiv2025

A V-ATPase complex, required for biogenesis of a lysosome-related organelle (LRO) in Tetrahymena thermophila, disassembles during LRO maturation

Lysosome-related organelles (LROs) are a heterogeneous family of organelles found in many cell types, whose significant similarities to lysosomes include their acidification by vacuolar-type ATPases (V-ATPases). However, some organelles with hallmarks of LROs are nonetheless non-acidic. Here we investigate this poorly understood phenomenon using the ciliate Tetrahymena thermophila, which have prominent secretory LROs called mucocysts. Using three different approaches, we show that mature mucocysts, poised for exocytosis, are non-acidic. Nonetheless, a specific V-ATPase a-subunit is targeted to mucocysts and is indispensable for mucocyst biogenesis and secretion. Consistent with this, immature mucocysts in the cytoplasm appear to be transiently acidified. The stage specificity of acidification can be explained by our finding that several canonical V-ATPase subunits are present in the immature, but not mature, mucocysts. Our data argue that a mucocyst-specific V-ATPase complex is targeted to newly-forming mucocysts and subsequently disassembles at a late stage in Tetrahymena LRO maturation, and that this depends on the AP-3 trafficking adaptor.

cell biology↗

bioRxiv2024

Inferring gene-pathway associations from consolidated transcriptome datasets: an interactive gene network explorer for Tetrahymena thermophila

Although an established model organism, Tetrahymena thermophila remains comparatively inaccessible to high throughput screens, and alternative bioinformatic approaches still rely on unconnected datasets and outdated algorithms. Here, we report a new approach to consolidating RNA-seq and microarray data based on a systematic exploration of parameters and computational controls, enabling us to infer functional gene associations from their co-expression patterns. To illustrate the power of this approach, we took advantage of new data regarding a previously studied pathway, the biogenesis of a secretory organelle called the mucocyst. Our untargeted clustering approach recovered over 80% of the genes that were previously verified to play a role in mucocyst biogenesis. Furthermore, we tested four new genes that we predicted to be mucocyst-associated based on their co-expression and found that knocking out each of them results in mucocyst secretion defects. We also found that our approach succeeds in clustering genes associated with several other cellular pathways that we evaluated based on prior literature. We present the Tetrahymena Gene Network Explorer (TGNE) as an interactive tool for genetic hypothesis generation and functional annotation in this organism and as a framework for building similar tools for other systems. Key PointsO_LIur approach integrates nearly 20-year-old microarray and contemporary RNA-seq datasets. C_LIO_LIrigorously compare co-expression clustering parametrization by way of computational controls. C_LIO_LICo-expression clustering identifies known and novel functionally associated genes in Tetrahymena. C_LI Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=119 SRC="FIGDIR/small/627356v2_ufig1.gif" ALT="Figure 1"> View larger version (35K): org.highwire.dtl.DTLVardef@1dbe655org.highwire.dtl.DTLVardef@1ef09aaorg.highwire.dtl.DTLVardef@63b670org.highwire.dtl.DTLVardef@5e9209_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗

bioRxiv2024

Diverse priming outcomes under conditions of very rare precursor B cells

Rare B cells can have special pathogen-recognition features giving them the potential to make outsized contributions to protective immunity. However, rare naive B cells infrequently participate in immune responses. We investigated how germline-targeting vaccine antigen delivery and adjuvant selection affect priming of exceptionally rare BG18-like HIV broadly neutralizing antibody-precursor B cells (~1 in 50 million) in non-human primates. Only escalating dose (ED) priming immunization using the saponin adjuvant SMNP elicited detectable BG18-like cells in germinal centers (GCs). All groups had strong GC responses, but only ED+SMNP and bolus+SMNP induced BG18-like memory B cells in >50% of animals. One group had vaccine-specific GC responses equivalent to ED+SMNP, but BG18-like memory B cells were rarely detected. Following homologous boosting, BG18-like memory B cells were more frequent in a bolus priming group, but had lower somatic hypermutation and affinities. This outcome was inversely associated with post-prime antibody titers, suggesting antibody feedback can significantly influence rare precursor B cell responses.

immunology↗

bioRxiv2024

High-resolution in vivo kinematic tracking with injectable fluorescent nanoparticles

Behavioral quantification is a cornerstone of many neuroscience experiments. Recent advances in motion tracking have streamlined the study of behavior in small laboratory animals and enabled precise movement quantification on fast (millisecond) timescales. This includes markerless keypoint trackers, which utilize deep network systems to label positions of interest on the surface of an animal (e.g., paws, snout, tail, etc.). These approaches mark a major technological achievement. However, they have a high error rate relative to motion capture in humans and are yet to be benchmarked against ground truth datasets in mice. Moreover, the extent to which they can be used to track joint or skeletal kinematics remains unclear. As the primary output of the motor system is the activation of muscles that, in turn, exert forces on the skeleton rather than the skin, it is important to establish potential limitations of techniques that rely on surface imaging. This can be accomplished by imaging implanted fiducial markers in freely moving mice. Here, we present a novel tracking method called QD-Pi (Quantum Dot-based Pose estimation in vivo), which employs injectable near-infrared fluorescent nanoparticles (quantum dots, QDs) immobilized on microbeads. We demonstrate that the resulting tags are biocompatible and can be imaged non-invasively using commercially available camera systems when injected into fatty tissue beneath the skin or directly into joints. Using this technique, we accurately capture 3D trajectories of up to ten independent internal positions in freely moving mice over multiple weeks. Finally, we leverage this technique to create a large-scale ground truth dataset for benchmarking and training the next generation of markerless keypoint tracker systems.

neuroscience↗

bioRxiv2024

Dose-dependent regulation of immune memory responses against HIV by saponin monophosphoryl lipid A nanoparticle adjuvant

The induction of durable protective immune responses is the main goal of prophylactic vaccines, and adjuvants play an important role as drivers of such responses. Despite advances in vaccine strategies, a safe and effective HIV vaccine remains a significant challenge. The use of an appropriate adjuvant is crucial to the success of HIV vaccines. Here we assessed the saponin/MPLA nanoparticle (SMNP) adjuvant with an HIV envelope (Env) trimer, evaluating the safety and impact of multiple variables including adjuvant dose (16-fold dose range), immunization route, and adjuvant composition on the establishment of Env-specific memory T and B cell responses (TMem and BMem) and long-lived plasma cells in non-human primates. Robust BMem were detected in all groups, but a 6-fold increase was observed in the highest SMNP dose group vs. the lowest dose group. Similarly, stronger vaccine responses were induced in the highest SMNP dose for CD40L+OX40+ CD4 TMem (11-fold), IFN{gamma}+ CD4 TMem (15-fold), IL21+ CD4 TMem (9-fold), circulating TFH (3.6-fold), bone marrow plasma cells (7-fold), and binding IgG (1.3-fold). Substantial tier-2 neutralizing antibodies were only observed in the higher SMNP dose groups. These investigations highlight the dose-dependent potency of SMNP in non-human primates, which are relevant for human use and next-generation vaccines.

immunology↗

bioRxiv2024

Dengue Virus Surveillance in Nepal Yields the First On-Site Whole Genome Sequences of Isolates from the 2022 Outbreak

BackgroundThe 4 serotypes of dengue virus (DENV1-4) can each cause potentially deadly dengue disease, and are spreading globally from tropical and subtropical areas to more temperate ones. Nepal provides a microcosm of this global phenomenon, having met each of these grim benchmarks. To better understand DENV transmission dynamics and spread into new areas, we chose to study dengue in Nepal and, in so doing, to build the onsite infrastructure needed to manage future, larger studies. Methods and ResultsDuring the 2022 dengue season, we enrolled 384 patients presenting at a hospital in Kathmandu with dengue-like symptoms; 79% of the study participants had active or recent DENV infection (NS1 antigen and IgM). To identify circulating serotypes, we screened serum from 50 of the NS1+ participants by RT-PCR and identified DENV1, 2, and 3 - with DENV1 and 3 codominant. We also performed whole-genome sequencing of DENV, for the first time in Nepal, using our new on-site capacity. Sequencing analysis demonstrated the DENV1 and 3 genomes clustered with sequences reported from India in 2019, and the DENV2 genome clustered with a sequence reported from China in 2018. ConclusionThese findings highlight DENVs geographic expansion from neighboring countries, identify China and India as the likely origin of the 2022 DENV cases in Nepal, and demonstrate the feasibility of building onsite capacity for more rapid genomic surveillance of circulating DENV. These ongoing efforts promise to protect populations in Nepal and beyond by informing the development and deployment of DENV drugs and vaccines in real time.

genomics↗

bioRxiv2024

Loss of circulating CD8α+ NK cells during human Mycobacterium tuberculosis infection

Natural Killer (NK) cells can recognize and kill Mtb-infected cells in vitro, however their role after natural human exposure has not been well-studied. To identify Mtb-responsive NK cell populations, we analyzed the peripheral blood of healthy household contacts of active Tuberculosis (TB) cases and source community donors in an endemic region of Port-au-Prince, Haiti by flow cytometry. We observed higher CD8 expression on NK cells in putative resistors (IGRA-contacts) with a progressive loss of these circulating cells during household-associated latent infection and disease. In vitro assays and CITE-seq analysis of CD8+ NK cells demonstrated enhanced maturity, cytotoxic gene expression, and response to cytokine stimulation relative to CD8- NK cells. CD8+ NK cells also displayed dynamic surface expression dependent on MHC I in contrast to conventional CD8+ T cells. Together, these results support a specialized role for CD8+ NK cell populations during Mtb infection correlating with disease resistance.

immunology↗