Biology subjects

Wang, K.

Publications and source records attributed to Wang, K..

At least 55 records · Page 3Linked to original sources

bioRxiv2026

Miniaturized subcutaneous cellular implants for sustained therapeutic protein delivery in resource-limited settings

Cell encapsulation offers a promising strategy for sustained therapeutic protein delivery, obviating the need for repeated injections. Among potential implantation sites, the subcutaneous space is particularly attractive for its accessibility and amenability to minimally invasive procedures. However, performance of subcutaneous devices reported to date has been limited due to various challenges including foreign body response (FBR) and inadequate mass transfer. Moreover, typical encapsulation devices require surgeries for implantation and retrieval, limiting their potential use in resource-limited settings. Here we present a miniaturized cell encapsulation platform comprising cells engineered to produce therapeutic proteins and an FBR-mitigating zwitterionic polyurethane nanofibrous membrane, in a thin cylindrical form factor compatible with applicator-based minimally invasive implantation and retrieval. Clonal mesenchymal stromal cells engineered to produce PGT121, a broadly neutralizing anti-HIV-1 antibody, were encapsulated and inserted subcutaneously, achieving long-term cell survival and sustained serum PGT121 concentrations for up to 36 weeks across multiple murine models. Cell-loaded devices retained therapeutic function after cryopreservation, supporting their potential use as an off-the-shelf product that can be centrally manufactured and implanted on-site without specialized infrastructure. The custom-designed applicator-based implantation and minimally invasive retrieval procedures were demonstrated in a more clinically relevant minipig model. These mini-"cellular factories" represent a translatable strategy for sustained delivery of biologic drugs in resource-limited settings. One Sentence SummaryAn insertable and retrievable mini cellular construct enables sustained protein delivery, supporting its potential use in resource-limited settings.

bioengineering↗

bioRxiv2026

Integrating longitudinal hyperspectral phenotyping with AI and GWAS to dissect barley waterlogging responses

Waterlogging is a major constraint on barley productivity, yet its dynamic, multi-phase nature makes it challenging to dissect using traditional phenotyping approaches. High-throughput phenotyping (HTP) platforms address this by enabling temporal, multi-sensor imaging of large populations, but generate complex datasets that demand new analytical frameworks. Here, we imaged 230 barley accessions over 14 days of waterlogging stress and seven days of recovery using visible, chlorophyll fluorescence, and hyperspectral sensors. Explainable AI was applied to classify stress responses into early stress, late stress, and recovery phases, achieving 86% classification accuracy, and to identify the hyperspectral indices most informative for each phase. Water index (WATER1) and structure insensitive pigment index (SIPI) emerged as primary predictors of stress response. Longitudinal genome-wide association studies (GWAS), using a treatment-by-marker interaction model, identified 236 significant loci across 12 linkage disequilibrium blocks, implicating candidate genes involved in oxidative stress regulation, transcriptional control, and auxin transport. MYB transcription factors were consistently identified across all stress phases, underscoring their central role in waterlogging adaptation. To support interpretation of longitudinal GWAS results, we developed 3D-QTLVis, an interactive visualisation tool that extends Manhattan plots across time, enabling clearer identification of dynamic genomic regions underlying stress tolerance.

plant biology↗

bioRxiv2026

Dual-channel whole-brain imaging reveals distinct dopamine and calcium dynamics in walking Drosophila

Simultaneous recording of intra- and extracellular neuronal signals across the brain during behavior is crucial for unraveling brain information processing. In Drosophila, large-scale recordings have been explored, yet simultaneous dual-channel whole-brain imaging remains a significant challenge. We developed a system combining a Fourier light-field microscope with dual-focal microlens arrays optimized for adult walking flies, extending imaging volume while maintaining resolution requirements. This optical system is further combined with a cross-modal 3D registration and segmentation pipeline to integrate functional and structural data. Using this system, we simultaneously measured brain-wide intracellular calcium activity and extracellular dopamine release during locomotion. We found that functional maps and neural dynamics for dopamine and calcium are distinct across the brain and within specific compartments, particularly in the mushroom body and central complex, aligning with their anatomical bases. Both calcium and dopamine representations of locomotion are distributed, yet they exhibit different patterns. Mushroom body compartments can be functionally categorized into two types based on their responses to specific locomotive actions. Forward walking or acceleration boosts activity in compartments innervated by PAM dopaminergic neurons, while dampening activity in those targeted by PPL1 dopaminergic neurons. Conversely, backward walking or deceleration heightens PPL1 activity while reducing PAM activity, consistent with the functions of these neurons in encoding approach and avoidance choices. Notably, single-compartment activity can reliably decode behavior choices. Our findings, spanning whole-brain, brain-region, and single-compartment, demonstrate the capability of our system to uncover neural dynamics across multiple scales and channels in behaving animals.

neuroscience↗

bioRxiv2026

Objective curriculum-guided design of multi-property proteins

Designing functional proteins that simultaneously possess multiple bio-chemical properties remains a significant challenge, as key protein properties, such as solubility, stability, binding affinity, and chemical resistance, are often interdependent or even conflicting. Current approaches typically attempt to jointly optimize multiple functional objectives in one shot, followed by extensive screening to identify rare feasible designs. Here, we introduce OCDesign, an objective curriculum-guided framework for multi-property protein design. OCDesign is based on the objective curriculum principle, i.e., the order in which objectives are introduced can shape the accessibility of functional solutions. In each design round of OCDesign, candidate sequences are generated in silico, assessed across multiple properties, selected based on Pareto-optimal trade-offs, and experimentally validated, with each experimental stage testing the role of the newly introduced objective within the curriculum. Using antibody-binding protein A as a model system, we show that one-shot optimization fails to yield functional designs, whereas a staged curriculum--progressing from solubility and structural consistency to binding affinity, and then to alkaline resistance--enables the design of proteins possessing multiple desired properties through substantially fewer wet-lab experiments. These results establish OCDesign as a practical computational-experimental strategy for organizing and integrating multiple objectives in protein design, and suggest that objective ordering is a key determinant of accessibility in high-dimensional design spaces.

bioengineering↗

bioRxiv2026

UcTCRp: a TCRβ-based framework for quantitative MAIT- and iNKT-associated repertoire-state profiling

MAIT and iNKT cells are conventionally identified using invariant or semi-invariant TCR chains, antigen-loaded tetramers, or transcriptomic phenotypes. These requirements limit their detection in public and clinical immune-repertoire datasets that contain only TCR{beta} sequences. Here we present UcTCRp, a TCR{beta}-only framework for profiling MAIT- and iNKT-associated repertoire states in bulk immune repertoires. UcTCRp integrates V-gene context and CDR3{beta} sequence features using a transformer-based representation pretrained on more than one million TCR{beta} sequences and supervised with curated cross-species MAIT, iNKT and conventional T cell references. The framework defines conserved model-informative TCR{beta} features, uses V-matched negative sampling to reduce germline-segment shortcuts, and generalizes across independent human and mouse datasets. In paired scRNA-seq/scTCR-seq datasets, UcTCRp recovered transcriptome-defined MAIT and iNKT cells and identified additional MAIT-like candidates supported by receptor evidence but missed by expression-only annotation. Bulk calibration against paired single-cell references and synthetic spike-in experiments established operating characteristics for repertoire-level abundance estimation. These results establish unpaired TCR{beta} repertoires as an actionable substrate for reconstructing unconventional T cell-associated immune states, enabling archived repertoire resources to be repurposed for systems-level studies of tissue immunity, disease and therapeutic response.

bioinformatics↗

bioRxiv2026

Rapid in vitro synthesis of DNA templates via Sidewinder for polyadenylated Hantavirus mRNA vaccine candidates

As the recent COVID-19 pandemic illustrated, zoonotic viruses and other pathogens pose a credible threat to public health. Recent advancements in vaccine technology, particularly mRNA vaccines, provide key tools for an effective and swift public health response. Although mRNA vaccines can be developed more quickly than traditional vaccines, fast and accurate construction of DNA templates for these vaccines remains a critical bottleneck. Using our novel DNA assembly technology, Sidewinder, we rapidly designed and built multiple mRNA vaccine candidates to guard against a potential outbreak of Hantavirus (ANDV). We successfully constructed the DNA templates from oligo pools and produced the mRNA for three vaccine candidates in just 2 days after delivery of the synthetic DNA oligos.

biochemistry↗

bioRxiv2026

The HOG MAPK - Transcription Factor CsAtf1 - CsErg5B Regulatory Module Mediates Conidial Germination and Fludioxonil Sensitivity in Colletotrichum siamense

Colletotrichum siamense is a predominant causal agent of anthracnose in rubber tree and numerous economically important crops, causing severe yield losses worldwide. Conidial germination represents a critical early step for successful infection, while the high-osmolarity glycerol (HOG) MAPK pathway and ergosterol biosynthesis individually govern fungal development, stress adaptation and fungicide responses. However, the molecular crosstalk between these two modules remains largely elusive in phytopathogenic fungi. Here, we identified CsErg5B, a sterol C-22 desaturase homolog, as a direct target of the HOG- regulated transcription factor CsAtf1 in C. siamense. CsErg5B was indispensable for ergosterol biosynthesis, conidial germination, appressorium formation, and full virulence. The {Delta}CsErg5B mutant showed increased conidiation but severely impaired germination, and exhibited elevated resistance to fludioxonil while hypersensitivity to azole fungicides. Epistasis analysis using the {Delta}CsErg5B/{Delta}CsCyp51G1 double mutant - where CsCyp51G1 serves as another downstream target of CsAtf1 - revealed that CsErg5B functions as the predominant downstream effector of CsAtf1 in modulating conidial development and fludioxonil sensitivity. Furthermore, overexpression of CsErg5B significantly rescued the defects in conidial germination and fludioxonil sensitivity in both {Delta}CsAtf1 and {Delta}CsPbs2 mutants. Taken together, our findings uncover a HOG MAPK - CsAtf1 - CsErg5B regulatory axis that connects HOG MAPK signaling to ergosterol homeostasis, thereby governing conidial germination and fungicide sensitivity in C. siamense. This study provides novel insights into the regulatory network underlying fungal development and fungicide response, and offers promising molecular targets for the integrated management of plant anthracnose.

microbiology↗

bioRxiv2026

Elevated conformational dynamics makes ACKR3 activation-prone and G protein-incompetent

The atypical receptor ACKR3 works together with the canonical chemokine receptor CXCR4 to drive cell migration along gradients of their shared agonist CXCL12. CXCR4 promotes chemotaxis by activating canonical G protein pathways and recruiting {beta}-arrestins. ACKR3 indirectly regulates CXCR4-mediated chemotaxis by scavenging CXCL12. Unlike canonical chemokine receptors, ACKR3 does not couple to G proteins and instead is 100% biased towards {beta}-arrestins. CXCR4 activation by CXCL12 is exquisitely sensitive to subtle changes in both receptor and ligand. By contrast, ACKR3 is activation-prone: it recruits {beta}-arrestins in response to many ligands and is much less sensitive to mutations, suggesting distinct activation mechanisms compared to CXCR4. To explore the basis of these differences, we compared the dynamics of ACKR3 and CXCR4 complexes with chemokines using molecular dynamic (MD) simulations. Ten-microsecond atomistic MD simulations revealed that CXCR4 adopts a stable active state when bound to WT CXCL12 but transitions to an inactive state when in complex with the antagonist variant, [P2G]CXCL12. By comparison, ACKR3 exhibits a variable transmembrane (TM) 6 state distribution and persistently "active" TM7 when complexed with either WT CXCL12 or [P2G]CXCL12, the latter retaining substantial agonistic activity at ACKR3. We further identified ligand-mediated residue interaction networks in the TM core that regulate TM6 and TM7 activation in CXCR4 but are absent or disrupted in ACKR3, resulting in less constrained receptor dynamics. These findings were validated by BRET-based assays with CXCL12 and ACKR3 mutants. Together, the data suggests that the unique conformational dynamics of ACKR3 govern its activation propensity, its ligand promiscuity, and its atypical effector coupling.

pharmacology and toxicology↗

bioRxiv2026

Tumor-Associated EDA-FN-Enriched Matrix Instructs Macrophage Behavior

IntroductionCancer progression is driven not only by tumor cells but also by interactions between the extracellular matrix (ECM), stromal cells, and immune cells within the tumor microenvironment (TME). Cancer-associated fibroblasts (CAFs) are major drivers of ECM remodeling, assembling ECM with aberrant organization. Extra domain A fibronectin (EDA-FN), a cellular FN containing an extra type III domain, is upregulated in the TME. EDA-FN regulates cellular behavior and has been associated with poor patient prognosis. Macrophages are among the most abundant immune cells within the TME, where they contribute to TME remodeling and inflammation to promote cancer cell invasion and metastasis. However, how tumor-associated matrix-specific cues regulate macrophage behavior remains largely understudied. PurposeHere, we developed a fibroblast-derived matrix platform that captures the structural imprint of tumor-associated EDA-enriched matrices and investigated how matrix-specific cues regulate macrophage behavior in the absence of ongoing soluble factor cues. MethodHuman mammary fibroblasts (HMFs) preconditioned in incubated low-serum media (lNC, or control) and MDA-MB231 metastatic breast cancer cell-conditioned media (mTCM) were cultured on polyacrylamide gels of 2 kPa and 20 kPa, respectively, followed by decellularization. Matrix organization, including fiber alignment, width, and intrafibrillar spacing, was quantified from confocal images. Decellularized EDA-FN-enriched matrices were subsequently reseeded with macrophages to assess macrophage morphology, phenotype, and matrix interactions. ResultsThe combined effects of tumor-derived soluble factors and pathological stiffness induced a CAF-like phenotype in HMFs, accompanied by cytoskeletal reorganization and microarchitectural alterations of EDA-FN-enriched matrices. Tumor-associated matrices exhibited increased alignment, narrower fiber width, and enlarged intrafibrillar spacing compared to control matrices. These aberrant, tumor-associated matrix-derived features were associated with altered macrophage behavior, including heterogeneous morphology, enhanced localized EDA-FN matrix loss beneath the cell body, and a hybrid phenotype with a shift toward a CD206-dominant profile. ConclusionsThese findings demonstrate the feasibility of obtaining EDA-FN-enriched matrices to isolate matrix-specific cues for investigating macrophage-ECM interactions. Furthermore, this platform can be leveraged to identify matrix-targeting therapeutic approaches for modulating macrophage function within the TME.

bioengineering↗

bioRxiv2026

Transgene Expression Kinetics and Replication Potential of Recombinant Adenovirus Serotype 4 in a Mouse Model and its Use as a Herpes Simplex Virus Vaccine

Human adenovirus serotype 4 (Ad4) is used as a replication-competent oral vaccine that safely and effectively prevents Ad4 respiratory illness in US military personnel. Recombinant Ad4 vaccine candidates elicit mucosal and systemic immune responses against respiratory viruses in hamsters, nonhuman primates, and humans. Although evaluation of Ad4 vaccine candidates in mice would be extremely useful given the large number of immunologic tools available, this has been limited by concerns about a lack of viral replication in these animals. Here we generated recombinant Ad4 vectors that express either luciferase (Ad4-Luc) or herpes simplex virus type 2 (HSV-2) glycoprotein D (Ad4-gD2) to identify transgene expression kinetics, the presence of Ad4 vector replication, and HSV-2 immune responses and protection against HSV-2 infection. Local luciferase activity was observed from 7 hours to 20 days after intranasal inoculation of BALB/c and humanized mice. Subsequent inoculations with Ad4-Luc showed reduced luciferase expression in BALB/c mice, but robust expression in humanized mice, suggesting an immune response to the vector in wild-type mice. Ad4 DNA, but not luciferase activity, was reduced in the lungs of BALB/c mice treated with cidofovir before inoculation with Ad4, implying that Ad4 replicated, albeit at a low level, in the lungs. Intranasal vaccination of mice with Ad4-gD2 resulted in HSV-2 neutralizing antibody in the serum, and after HSV-2 intravaginal challenge reduced disease scores, increased survival, and reduced shedding. Overall, the BALB/c mouse model is semi-permissive to Ad4 mucosal infection, but transgene expression is sufficient for the study of Ad4-based vaccine candidates. ImportanceMucosal surfaces serve as the primary site of infection and shedding for many viral pathogens. Immune responses at mucosal sites provide protection, but few mucosal vaccines are licensed. The oral replication-competent adenovirus serotype 4 (Ad4) vaccine is used to prevent respiratory illness in military recruits, has an extraordinary record of safety and efficacy and has been tested as a recombinant platform for other viruses. Further development of this vaccine platform has been partially hindered by the perceived inability to evaluate vaccine candidates in mice. Here we characterize recombinant Ad4 transgene expression kinetics and viral replication after inoculation at various sites and show protection against herpes simplex virus type 2 (HSV-2) genital disease in mice after intranasal vaccination. We show that Ad4 can induce protective efficacy, even in a semi-permissive mouse model, suggesting this is a promising vector for HSV-2 and potentially other viral pathogens.

immunology↗

bioRxiv2026

Increased medial collagen enhances aortic resilience against mural delamination from hydraulic fracturing

The aorta, normally resilient to hemodynamic stresses, becomes vulnerable to structural failure due to diverse conditions that weaken the wall. We injected fluid into excised specimens of human ascending aorta with pressure monitoring to quantify the impact of clinical and histological factors on mural damage. Two modes of medial injury emerged with distinct pressure tracings. Extravasation was characterized by diffuse infiltration of fluid with widespread damage of smooth muscle cells and collagen fibers but limited separation of elastic lamellae. By contrast, delamination was characterized by marked separation of elastic lamellae along a single plane with damage to cells and fibrillar matrix restricted to adjacent laminae. Aging, aortic dilatation, and family history associated with lower pressures causing delamination, whereas a diagnosis of hypertension associated with higher pressures suggesting resilience to dissection. Collagen fraction adjacent to delamination correlated with higher pressures as did decreased smooth muscle cell density and increased glycosaminoglycan fraction, although several clinical and histological variables were interrelated. Protein cross-linking strengthened and enzymatic digestion of collagen weakened the aortic wall, while acute cell lysis with detergent had no effect. We conclude that increased functional medial collagen has an adaptive protective role in aortic remodeling rather than signifying medial degeneration.

bioengineering↗

bioRxiv2026

ProteinFlux: accurate, rapid and scalable generative prediction of protein dynamics driven by post-translational modifications

The function of proteins, the building blocks of life, in health and disease depends not only on their 3D-conformational states but most importantly on the dynamic transition between states controlled by a wide array of post-translational modifications (PTMs). Recent major advances have been made in our ability to predict static 3D structures; however, understanding and predicting the impact of PTMs on protein conformational dynamics remains a major question and challenge in the field. Molecular dynamics (MD) simulation remains the major computational approach for studying protein dynamics. However, the high computational cost, lack of integration of PTMs as conditioning inputs and inefficient generation of continuous protein dynamics largely precludes PTM-regulated conformational dynamics and the study of slow conformational processes. To address this critical bottleneck, we developed ProteinFlux, a flow-matching generative framework that links PTM-conditioned conformational dynamics to evolutionary constraints encoded by PTM sites. Evolutionary information plays a critical role in capturing conformational dynamics beyond sequence identity, and PTM sites inherently encode evolutionary constraints critical to protein functional regulation. We therefore built FluxSite, a dual-modal PTM site predictor that integrates sequence evolutionary information and 3D structural features to generate a continuous conditional signal encoding conservation and functional importance for each predicted site. FluxSite achieves robust generalization across 18 PTM types and 30 disease-associated proteomes. ProteinFlux generates phosphorylation-conditioned, all-atom conformational trajectories across diverse protein fold classes, faithfully reproducing both thermodynamic properties such as free energy landscapes and kinetic features such as conformational transition pathways. It outperforms state-of-the-art predictors while achieving inference speeds several orders of magnitude faster than traditional MD. In addition, we introduce DynaMo-phos, a benchmark dataset of phosphorylated protein MD simulations. Together, ProteinFlux, FluxSite and DynaMo-phos provide a scalable, high-throughput platform for elucidating PTM-driven conformational mechanisms, with potential applications across allosteric drug design, functional annotation of disease-associated modifications and mechanism-guided therapeutic development.

bioinformatics↗

bioRxiv2026

LongAllele: a joint inference framework for allele-specific analysis on long-read bulk and single-cell RNA sequencing

Allele-specific analysis from RNA-seq is a powerful approach to characterize cis-regulatory effects. However, existing methods remain limited in both haplotype inference and allelic testing. Their haplotype-inference workflows separate variant calling, haplotype phasing, and read-haplotype assignment into sequential steps, failing to fully exploit within-read single-nucleotide variant (SNV) linkage information and propagating errors into downstream allelic analysis. At the testing stage, they ignore non-phasable reads lacking heterozygous SNVs, biasing calls and inflating false positives, and remain incomplete across gene-, isoform-, and local-event-level variant effects. Here, we present LongAllele, a statistical framework that employs an expectation-maximization algorithm to jointly infer heterozygous variants, haplotype structure, and read-haplotype assignments from long-read bulk and single-cell RNA sequencing. LongAllele further introduces phasability-aware testing that explicitly accounts for non-phasable reads, avoiding inflated false-positive calls when haplotype information is incomplete. It also enables comprehensive allelic testing across gene-level allele-specific expression (ASE), isoform-level allele-specific transcript usage (ASTU), and local-event-level haplotype-associated exon and junction usage (HAEU and HAJU), providing a multi-scale view of cis-regulation across biological contexts. We applied LongAllele to long-read RNA-seq datasets spanning GTEx (multi-tissue bulk), peripheral blood mononuclear cells (single-cell), human hippocampus (single-nucleus), and human cortex from two Alzheimers disease (AD) case-control cohorts (bulk, Oxford Nanopore and PacBio). LongAllele consistently revealed greater context dependence in expression-level than isoform-level allelic regulation across tissues, cell types, and disease states, and pinpointed high-impact regulatory variants including rare splice-site mutations missed by standalone variant callers. It further showed that purifying selection constrains allelic imbalance at both gene and isoform levels and resolved AD-associated variant effects in individual transcriptomes across long-read platforms.

bioinformatics↗

bioRxiv2026

Microglia-derived IL-18 remodels hippocampal plasticity to constrain traumatic fear memory

Post-traumatic stress disorder (PTSD) involves complex neuroimmune-synaptic crosstalk in the hippocampus. Here we show that interleukin-18 (IL-18), an extensively studied pro-inflammatory cytokine, serves a protective role against traumatic fear memory through a microglia-to-neuron signaling axis. Traumatic stress induces sustained upregulation of IL-18 in the hippocampus. Exogenous IL-18 administration attenuates fear memory, whereas blockade of IL-18 signaling exacerbates it. Mechanistically, microglial-derived IL-18 acts on neuronal IL-18R1 to restore stress-impaired synaptic plasticity and reduce perineuronal net density, thereby facilitating structural synaptic remodeling. In addition, IL-18 modulates the synaptic organization of fear memory-encoding engram cells within hippocampal ensembles. Together, these findings redefine IL-18 as a homeostatic regulator of post-trauma hippocampal synaptic function and identify the hippocampal IL-18 pathway as a potential therapeutic target for PTSD.

neuroscience↗

bioRxiv2026

One-pot parallel Sidewinder construction from oligo pools

Reliable and cost-effective de novo DNA production at scale has become increasingly important to studying and engineering biology. Double-stranded DNA is constructed from short synthetic single-stranded DNA oligonucleotides synthesized either individually or as a pool. Oligonucleotide pools offer substantially reduced costs at the sacrifice of yield and individual oligo isolation, making efficient multiplexed DNA construction from pools a complex engineering challenge, yet one which promises to reduce cost, labor, and turnaround time if solved. Here we introduce Oligo Pool Sidewinder assembly, which enables one-pot, parallel assembly of hundreds of DNA fragments simultaneously into dozens of defined constructs with high fidelity from oligo pools. We pair a computational workflow for string-based bespoke oligo design with a set of construction rules for highly multiplexed assembly. We demonstrate recovery of individual sequences from the pool by construct-specific amplification with misconnection rates as low as 1 in 10. This high fidelity for connection enables hundreds of oligos to co-assemble in a single reaction. Further, we show universal amplification of libraries of defined target sequences in a single PCR and extend the approach through in vitro hierarchical assembly to construct a large 12.5-kilobase synthetic linear DNA product.

molecular biology↗

bioRxiv2026

Hypermorphic TaARF4 shapes wheat architecture by repressing SPL-mediated developmental timing

Integrating spatial morphogens with temporal developmental clocks is fundamental to optimizing plant architecture and crop yield, yet their molecular interface remains elusive. Here, we characterize Branched shoot 1 (Bsh1), a semi-dominant wheat mutant exhibiting non-canonical upper-aerial branching and aberrant spike development, caused by a T265I substitution in the DNA-binding domain of the auxin response factor TaARF4-A2. Unlike flanking mutations governing protein stability in basal land plants, this central substitution uniquely converts TaARF4-A2 into an auxin-insensitive hypermorphic repressor. The mutant protein disrupts auxin-cytokinin homeostasis and markedly enhances the native repression of SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) transcription factors, the core timers of developmental phase transitions. This spatial and temporal uncoupling unleashes upper axillary buds from dormancy, promoting aerial branching and diverting resources from reproductive development. Our findings demonstrate how a conserved spatial morphogen effector was evolutionarily rewired in polyploid wheat to dictate the temporal SPL clock, orchestrating species-specific shoot architectural innovation.

plant biology↗

bioRxiv2026

Immunization With Herpes Simplex Virus Nanoparticles Targeting Both Attachment and Fusion Protect Against Infection

Herpes simplex virus 2 (HSV-2) is associated with genital ulcers, neonatal encephalitis, increased risk of HIV infection, and dementia. There is no licensed HSV-2 vaccine. We developed nanoparticles displaying the HSV-2 attachment protein gD and fusion mediation protein complex gH/gL. Immunization of mice and non-human primates elicited high levels of neutralizing antibodies. Vaccination conferred robust protection in mice, preventing disease and nearly eliminating infection and shedding following HSV-2 challenge. While gD induced high neutralizing antibody titers, gH/gL contributed substantially to protection despite lower neutralization titers. Instead, gH/gL immunization generated strong fusion-blocking responses which were an important correlate of protection, showing that standard neutralization assays incompletely capture the importance of fusion-blocking activity. These findings demonstrate that targeting both HSV-2 attachment and fusion elicit complementary mechanisms for protection from infection and that neutralizing antibody alone may be insufficient for protection. Overall, these results present an innovative strategy for an HSV-2 vaccine.

immunology↗

bioRxiv2026

Origin and evolution of grapevine genomes

Grapevines (Vitis) belonging to grape family (Vitaceae) are symbolic fruit crops pivotal to human civilization. The evolutionary history of grapevines divergent from other Vitaceae plants remains mysterious, requiring a family-wide whole-genome phylogenomic analysis. Here, we conduct chromosome-level phylogenomics to investigate the origin and evolution of grapevines using 29 genome assemblies of five genera Vitis, Parthenocissus, Ampelopsis, Tetrastigma, and Cissus, 27 of which are newly released in this study. Phylogenomic and macrosynteny analysis unanimously support Ampelopsis as a sister lineage to Parthenocissus, placing both closer to Vitis, with introgression and incomplete lineage sorting contributing to these relationships. Ancestral genome reconstruction delineates the major chromosome rearrangement events in Vitaceae karyotype evolution, highlighting the conserved karyotype in Vitis and the extensive karyotypic reorganization in Tetrastigma and Cissus. Pan-3D genome analysis highlights the contributions of structural variants (SVs) to the variation of A/B compartments and topologically associated domains (TADs), revealing a strong purifying selection of SVs at TAD boundaries. We further demonstrate that Helitron transposons drive the expansion and expression regulation of NLR immune-receptor genes in Vitis. Importantly, we discovered an NLR gene VbRpv35 from wild grapevine V. bellula resistant to downy mildew (DM), whose heterologous expression in V. vinifera confers enhanced DM resistance. Taken together, we provide phylogenomic insight into the origin and evolution of grapevines and valuable resources for grapevine improvement and understanding angiosperm evolution.

genomics↗