Biology subjects

Li, H.

Publications and source records attributed to Li, H..

At least 127 records · Page 7Linked to original sources

bioRxiv2026

Circadian clock gates retinal regeneration by orchestrating Cxcl12-dependent immune coordination

The circadian clock orchestrates tissue homeostasis and repair, yet its role in central nervous system (CNS) regeneration remains largely unexplored. Here, we identify the circadian clock as an essential regulator of adult zebrafish retinal regeneration, a CNS model. Retinal injuries induced at distinct circadian times elicit differential Muller glia (MG) reprogramming and progenitor proliferation, both of which exhibit robust diurnal fluctuations. Disrupting circadian rhythms--via constant darkness (DD) or day-night reversal (DL)--suppresses MG reprogramming, MG-derived progenitor cell (MGPC) formation and neuronal regeneration, concomitant with dampened retinal immune responses. Notably, intravitreal immune stimulation restores MGPC numbers in the retina under DD conditions, linking immune activation to circadian-regulated regeneration. Single-cell RNA-seq reveals that DD disrupts MG reprogramming trajectories while inducing unfolded protein response (UPR) and suppressing ATP/protein synthesis. Moreover, clock disruption alters microglia heterogeneity, and cell-cell communication analysis identifies the Cxcl12-Cxcr4 signaling as a key chemotactic axis between MG/endothelial cell and immune populations. Mechanistically, Bmal1b directly binds E-box motifs in the cxcl12a/12b promoters, driving their rhythmic transcription to orchestrate the immune response after injury. Importantly, exogenous Cxcl12a partially restores both immune and regenerative responses in clock-disrupted retinas, establishing the Cxcl12-Cxcr4 axis as a circadian-immune checkpoint for retinal repair. Collectively, our findings reveal a novel paradigm in which the circadian clock gates CNS regeneration through Cxcl12-mediated immune coordination, offering potential therapeutic insights for CNS repair in mammals.

neuroscience↗

bioRxiv2026

Intact learning and memory in mice incapable of de novo myelination

Motor skill learning stimulates and requires generation of oligodendrocytes (OLs) from their precursors (OLPs) in the adult mouse brain, but the functional role(s) of the newly formed OLs is not known. We asked whether new compact myelin sheaths are required, by genetic block of myelin basic protein (MBP) synthesis in adult OLPs and their newly-differentiating OL progeny, using tamoxifen-inducible Cre-lox recombination. Newly-differentiating OLs in these Mbp-cKO mice are unable to assemble compact myelin or normal nodes of Ranvier. Despite this, Mbp-cKOs learned a motor skill just as well as their wild type littermates. They also demonstrated normal contextual fear conditioning. Therefore, neither motor nor fear learning depends on rapid saltatory conduction in newly-myelinated circuits. Mbp-cKOs also formed normal long-term motor and contextual fear memories. Moreover, OL lineage-specific knockout of Monocarboxylate transporter-1 (Mct1), believed to be responsible for transferring metabolic substrates from OLs into axons, did not affect learning or memory consolidation. Myelin regulatory factor (Myrf)-cKOs, in which newly-differentiating OLs die and are rapidly eliminated, confirmed that newly formed OLs are required for learning and memory. Together, the data suggest that learning and memory depends on a non-canonical property of pre-myelinating or myelinating OLs, distinct from myelins cardinal role in speeding action potentials.

neuroscience↗

bioRxiv2026

Validation of MHPC512: A Publicly Available Special-Purpose Supercomputer for Molecular Dynamics Simulations of Biomolecular Systems

MHPC512 is a massively parallel, special-purpose supercomputer designed primarily for atomic-level molecular dynamics (MD) simulations of biomolecular systems. It comprises 512 processor units interconnected by a high-speed three-dimensional torus network and employs a custom chip architecture that uses 35-bit fixed-point arithmetic to accelerate computation while controlling precision loss within an acceptable margin. The preprocessor is compatible with GROMACS and AMBER input formats and supports widely used biomolecular force fields (including CHARMM, AMBER, and OPLS/AA), the Neutral Territory method for short-range nonbonded interactions, the k-space Gaussian Split Ewald method for long-range electrostatics, and multiple thermostats, barostats, and integrators. We present a three-tier validation protocol--comparing static energy and virial components, examining ensemble distributions (NVE, NVT, NPT), and evaluating long-time statistical properties--demonstrating that MHPC512 reproduces results consistent with GROMACS and AmberTools. Application examples, including bulk water, dipeptide conformational sampling, folding of fast-folding peptides, membrane-protein systems, lipid self-assembly, and GPCR conformational transitions, further confirm its reliability. MHPC512 has been deployed at multiple supercomputing centers and is publicly accessible, representing a significant advance in high-throughput, large-scale biomolecular MD simulations.

Molecular Biology↗

bioRxiv2026

Lineage-specific chromatin poising enforced by ETS-IRF composite elements determines the divergent interferon responses of plasmacytoid dendritic cells and epithelial cells

Plasmacytoid dendritic cells (pDCs) produce robust type I interferons (IFN-I) within hours of viral sensing, while epithelial cells at mucosal surfaces mount a delayed response dominated by type III interferons (IFN-III). Both cell types express pattern recognition receptors that activate similar downstream transcription factors, yet they produce distinct subsets of IFNs. The mechanisms underlying these differences have remained unclear. Here, using Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) in primary human pDCs and intestinal epithelial cells, we show that IFN-I and IFN-III gene loci carry opposing, constitutively established chromatin accessibility landscapes that determine cell-type-specific interferon induction. The IFN-I locus is broadly open in pDCs and constitutively closed in epithelial cells, while the IFN-III locus displays the reciprocal pattern. Motif enrichment analysis of accessible regions at the IFN-I locus in pDCs revealed unexpected and significant enrichment of ETS family binding motifs alongside IRF motifs, which determines the cell-type-specific locus accessibility. The ETS factor PU.1 and IRF8 bind IFN-I promoters, at composite ETS-IRF elements positioned at the Positive Regulatory Domain IV (PRDIV) site of IFNB1 promoter and adjacent to the TATA-proximal IRF motif of IFNA promoters. IFNL gene promoters lack ETS recognition sequences. PU.1-IRF8 composite factor binding extends across intergenic regions of the IFN-I locus, where candidate enhancer elements marked by H3K4me1, H3K27ac, and RNA Pol II occupancy were identified. We propose that this network of ETS-IRF composite-element-anchored enhancers maintains the IFN-I locus in a constitutively poised state in pDCs, licensing the rapid and robust IFN-I response that defines pDCs. In epithelial cells, the absence of PU.1 and IRF8 renders the IFN-I locus epigenetically silent, while the IFN-III locus is constitutively open. Despite this, the delayed IFN-III gene expression in epithelial cells is due to intrinsically weaker promoter activity relative to IFN-I. These findings reveal that the divergent IFN induction of pDCs and epithelial cells is determined by the chromatin architecture prior to infection. Overall, these observations show that lineage-specific ETS-IRF regulatory factors and promoter strength determine the cell-type-specific IFN activation.

immunology↗

bioRxiv2026

M6A-modified circEZH2 Protects Endothelial Cells from Senescence and Suppresses Atherosclerosis by Stabilizing ZNF326

BACKGROUNDEndothelial cell senescence induces endothelial dysfunction, thereby contributing to atherosclerosis progression. Circular RNAs (circRNAs) play diverse roles in multiple physiological and pathological processes. N6-methyladenosine (m6A) is the most abundant internal RNA modification in eukaryotic RNAs and dynamically regulates RNA fate and function. However, the functions and therapeutic potential of m6A-modified circRNAs in endothelial cell senescence remain unknown. METHODSm6A-modified circRNAs associated with endothelial cell senescence were screened by circRNA expression and m6A-circRNA microarray profiling of endothelial cells and mouse aortic intima. circEZH2 expression was validated in endothelial cells, vascular tissues, and human atherosclerotic plaques by RT-qPCR, and RNA fluorescence in situ hybridization. The role of circEZH2 in endothelial senescence and atherosclerosis was assessed in vitro and in vivo. RNA pull-down, mass spectrometry, RNA immunoprecipitation, co-immunoprecipitation, ubiquitination assays, and rescue experiments were used to define the underlying mechanism. RESULTSWe identified A novel m6A-modified circRNA, circEZH2, that was downregulated in the aged aortic intima and advanced plaques. CircEZH2 was stabilized by m6A reader IGF2BP2. Endothelial cell-specific overexpression of circEZH2 delayed senescence and suppressed atherosclerosis progression. At the cellular level, circEZH2 overexpression delayed senescence, decreased p53/p21 levels and increased angiogenic activity of endothelial cells, while circEZH2 knockdown exhibited the opposite effect. Mechanistically, circEZH2 functions as a scaffold to promote USP37-mediated deubiquitination, thereby stabilizing ZNF326. Moreover, endothelial cell-specific knockdown of ZNF326 counteracts the anti-senescent and anti-atherosclerotic effects mediated by circEZH2 overexpression. CONCLUSIONSIn summary, the present study identifies circEZH2 as a novel suppressor of endothelial cell senescence, highlighting its potential as a therapeutic target for age-related atherosclerosis. GRAPHIC ABSTRACTA graphic abstract is available for this article. O_FIG O_LINKSMALLFIG WIDTH=177 HEIGHT=200 SRC="FIGDIR/small/730538v1_ufig1.gif" ALT="Figure 1"> View larger version (78K): org.highwire.dtl.DTLVardef@d3a586org.highwire.dtl.DTLVardef@1180c1forg.highwire.dtl.DTLVardef@1c3d832org.highwire.dtl.DTLVardef@a6d424_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphic abstract.C_FLOATNO Schematic model of m6A-modified circEZH2 regulation in endothelial cell senescence and atherosclerosis. In young endothelial cells, IGF2BP2 is highly expressed and recognizes m6A-modified circEZH2, thereby maintaining its RNA stability. CircEZH2 stabilizes ZNF326 protein through USP37-mediated deubiquitination, which leads to suppression of p21 and p53, delays endothelial cell senescence, ameliorates endothelial dysfunction, and ultimately suppresses the progression of atherosclerosis. C_FIG What Are the Clinical Implications?This study identifies circEZH2 as a novel m6A-modified circular RNA that is reduced in the aged aortic intima and in endothelial cells within advanced atherosclerotic plaques. Endothelial circEZH2 overexpression delays endothelial cell senescence, preserves endothelial function, and suppresses atherosclerotic lesion formation, supporting an important role for circEZH2 in vascular aging-associated atherosclerosis. Mechanistically, circEZH2 acts as a scaffold to enhance USP37-mediated deubiquitination and stabilization of ZNF326, while endothelial ZNF326 knockdown counteracts the anti-senescent and anti-atherosclerotic effects of circEZH2. These findings reveal the circEZH2-ZNF326 axis as a previously unrecognized mechanism regulating endothelial senescence and atherosclerosis progression. Our work supports the potential of circEZH2-based gene therapy as a novel therapeutic approach for atherosclerosis.

cell biology↗

bioRxiv2026

Dynamic Gating Mechanism of the b0,+AT-Mediated Arg Transport: Insights from ASMD Simulations

Heteromeric amino acid transporters (HATs) mediate essential amino acid flux across membranes, but the molecular dynamics of substrate translocation remain poorly defined for many family members. Here, using conventional and adaptive steered molecular dynamics (cMD and ASMD) simulations, we identify residue W230 in the b0,+AT transport channel as a dynamic gate that regulates arginine (Arg) influx through side chain flipping. By integrating dynamic network analysis with dynamical cross-correlation of residue motions, we show that regulatory signals propagate from the Arg binding site through transmembrane helix 5 (TM5), a connecting loop, and TM6 to reach W230. We propose a dynamic gating mechanism for b0,+AT - mediated amino acid transport. Arg binding at V186 triggers signal propagation that enhances cooperative interactions between W230 and Arg, driving the side chain flipping of W230. Our findings reveal a dynamic gating mechanism underlying b0,+AT - dependent Arg transport and suggest that residue-triggered side chain reorientation may represent a conserved and efficient strategy in transporter function. Author SummaryAmino acids are the essential building blocks of life, and their transport across cell membranes is vital for nutrition and cellular signaling. Heteromeric amino acid transporters (HATs) mediate this process, yet how they physically move substrates through the protein at the atomic level remains poorly understood. In this study, we used advanced computer simulations to observe, in unprecedented detail, how b0,+AT--a key HAT member--transports the amino acid arginine. Our simulations revealed that a single residue, tryptophan 230 (W230), functions as a molecular gate: its side chain flips open to allow arginine to pass and then closes behind it, ensuring one-way traffic into the cell. We further discovered that the initial binding of arginine sends a signal through specific structural elements (helices and loops) to trigger this gate opening. This work not only uncovers a dynamic gating mechanism for b0,+AT but also suggests that similar side-chain flipping events may represent a common and efficient strategy used by other transporters to control substrate movement. Our findings provide a new framework for understanding transporter function and could inform future drug design targeting these critical membrane proteins.

biophysics↗

bioRxiv2026

A U1-U3 snRNA-snoRNA interaction couples SF3B1 mutation to chromatin-state rewiring and genome instability

Mutations in spliceosome factors such as SF3B1 are recurrent across human diseases, including myelodysplastic syndromes and leukemia1-4, yet splicing defects alone do not fully explain the widespread chromatin alterations and genome instability in mutant cells5. Here, by comprehensively mapping snRNA-directed RNA-RNA interactions, we identify two previously unrecognized interaction motifs in U1 snRNA beyond canonical 5' splice-site pairing6,7. These motifs enable U1 RNA to i) bind intronic and other chromatin-associated RNA (caRNA) regions outside of splice sites, and ii) base pair specifically with snoRNA. We uncover a U1-U3 snRNA-snoRNA interaction that recruits the H3K36 methyltransferase SETD2 to caRNA, promoting gene-body H3K36me3 and antagonizing H3K27me3 to modulate chromatin accessibility. The snRNA-snoRNA interface is essential for this previously unrecognized layer of chromatin and transcriptional regulation mediated through SETD2. SF3B1 mutation enhances U1-U3 binding and increases the association of the U1-U3 complex with caRNA, driving chromatin-accessibility remolding, R-loop formation, DNA damage, and copy-number abnormalities that promote tumorigenesis. A U1-specific 2'-O-methoxyethyl antisense oligonucleotide that selectively blocks U1-U3 pairing suppresses these genomic abnormalities, reduces leukemic infiltration, and prolongs survival in xenograft and patient-derived models, establishing pathological snRNA-snoRNA rewiring as a critical driver of SF3B1-mutant leukemogenesis.

cell biology↗

bioRxiv2026

Piezo1 transduces mechanical signals to inhibit osteoclast fusion and coordinate bone homeostasis

Osteoclasts originate from bone marrow-derived macrophages, and their maturation relies on fusion of pre-osteoclasts into mature osteoclasts that maintain bone homeostasis. Previous studies established that mechanical signals regulate osteoblast activity in bone homeostasis, although whether such signals regulate bone homeostasis by acting on osteoclasts remains unclear. Herein, membrane tension decreased during pre-osteoclast fusion, accompanied by reduced Piezo1. This suggests that mechanical stimulation inhibits fusion of monocytes into osteoclasts through Piezo1. Piezo1-knockout monocytes (CTSKCre; Piezo1fl/fl) attenuated the anabolic effect of exercise on bone mass in vivo, whereas shear stress inhibited osteoclast fusion in vitro. Piezo1 activation elevated E-cadherin, which anchors Merlin. This led to hyperactivation of the Yes-associated protein (YAP) signaling pathway, subsequently activating TAX1BP1 and suppressing NF-{kappa}B signaling as well as osteoclast differentiation and maturation. Thus, physical exercise activates a Piezo1-E-cadherin-Merlin-YAP axis that prevents osteoclast fusion, presenting a druggable mechanotransduction pathway for osteoporosis.

cell biology↗

bioRxiv2026

Transcription factor CCTF1 plays a decisive role in regulating the proteasome activity during archaeal cell division

Archaea of the order Sulfolobales exhibit a highly ordered cell cycle progression similar to that of eukaryotes. It has been demonstrated that degradation of the cell division protein CdvB by the proteasome controls the progression of cell division. However, how the proteasome itself is regulated during the cell cycle is not fully understood. Recently, the cyclically expressed ArsR family transcription factor CCTF1 (cell cycle transcription factor 1) was shown to represses expression of PAN (proteasome-activating nucleotidase) in Sulfolobus acidocaldarius. Here, using biochemical approaches, comparative transcriptomics and proteomics, we provide further insights into the CCTF1 function and show that it regulates PAN expression in Saccharolobus islandicus by binding to an AT-rich palindromic sequence within the pan promoter. We also reassessed the role of the cyclically expressed protein kinase aCcrK in regulation of proteasome activity and conclude that CCTF1, rather than aCcrK, is the primary factor controlling the proteasome activity. These findings advance our understanding of the proteosome-mediated cell cycle regulation in archaea.

microbiology↗

bioRxiv2026

Long-read RNA-seq resolves isoform-level and context-specific regulatory architecture of complex traits in cattle

Traditional short-read RNA-seq lacks the resolution to fully capture full-length isoforms and complex alternative splicing, leaving a "missing regulation" gap in existing molecular atlases. Here, we present a population-scale, multi-omics dissection of bovine complex traits using matched deep whole-genome sequencing (30x), long-read (ONT) and short-read RNA-seq, as well as metabolome data from 432 dairy cows across four distinct lactation stages. We expanded the bovine transcript atlas with 13,177 novel isoforms and fine-mapped 1,088,900 regulatory effects across 11 diverse molecular phenotypes. Notably, long-read mapping uncovered 606 genes with isoform expression quantitative trait loci (12.8%, eQTL) and 1,116 genes with detailed splicing QTL (sQTL) (31.8%) that were missed by conventional short-read mapping. We further showed that lactation-specific regulation was profoundly mediated by the metabolic microenvironment (46.8%) and cellular composition (4.3%). Across genome-wide associations (GWAS) of 90 bovine complex traits, isoform-level and context-specific regulatory effects captured GWAS loci missed by short-read eQTL and sQTL analyses, increasing colocalized loci from 35.2% to 60.3%. These regulatory variants also exhibited evolutionary constraints with human immune and metabolic loci. Our study establishes an invaluable resource (https://cattleblr.farmgtex.org) demonstrating that long-read transcriptomics is essential for resolving the complexity of regulatory mechanisms underlying mammalian physiology.

genetics↗

bioRxiv2026

Linezolid Acts as a Selective Inhibitor of the JAK2V617F Mutation

The JAK2V617F (JAK2VF) driver mutation is found in 95% of patients with polycythemia vera (PV), a progressive myeloproliferative neoplasm. Current treatments suppress excessive hematopoiesis but lack specificity for targeting JAK2VF cells, are unable to deplete mutant stem/progenitor cells and ultimately result in drug resistance. We discovered that the FDA-approved antibiotic, linezolid (LZD), ameliorates the PV phenotype across multiple model systems. LZD suppressed cell proliferation and STAT5 signaling, altered the cell cycle, and increased apoptosis of JAK2VF-harboring human erythroleukemia cells, but not in wild-type acute leukemia cells. Computational modelling indicated that LZD interacts specifically with mutant JAK2VF but not with wild-type JAK2 protein. We further showed that, in JAK2VF mice that faithfully recapitulate human PV, LZD mitigates disease burden by selectively targeting JAK2VF stem cells thereby normalizing spleen size and blood counts. LZD also inhibited hematopoietic colony formation by patient-derived peripheral blood mononuclear cells, with the more primitive progenitors being preferred targets. Importantly, LZD selectively decreased JAK2VF+ colony numbers, without impacting wild-type JAK2 colonies. In all, the data provide a firm foundation for evaluating LZD-like molecules as an effective therapy for PV and other myeloproliferative neoplasms. Key pointsO_LILinezolid acts as a JAK2V617FIZselective inhibitor in PV mouse models and PV patient samples while sparing wildIZtype hematopoiesis. C_LIO_LILinezolid acts directly on JAK2V617F hematopoietic stem cells. C_LI

cancer biology↗

bioRxiv2026

Intra-Abdominal Bowel Dilation in Experimental Gastroschisis is Associated with a Modifiable Transcriptomic Program of Intestinal Dysfunction

STRUCTURED ABSTRACTO_ST_ABSObjectiveC_ST_ABSTo characterize intestinal transcriptional profiles in gastroschisis, their temporal evolution, and response to fetal intervention. Summary Background DataGastroschisis causes significant intestinal dysfunction, with intra-abdominal bowel dilation clinically shown to correlate with worse outcomes. While inflammation and neurovascular impairment have been implicated, genome-wide transcriptional characterization of disease severity remains lacking. MethodsUsing a fetal ovine model of complex gastroschisis, in which all gastroschisis animals demonstrated significant intra-abdominal bowel dilation at term, bulk RNA sequencing was performed on proximal small intestinal tissue from mid-gestation and term fetuses across three groups: normal, gastroschisis, and prenatally repaired gastroschisis. Differential gene expression (FDR [≤] .05, |log2 fold change| [≥] 1.5) and pathway enrichment analyses were performed, with targeted interrogation of extracellular matrix (ECM), enteric nervous system (ENS), angiogenic, and inflammatory pathways. ResultsAt mid-gestation, gastroschisis intestine showed minimal transcriptional differences (150 differentially expressed genes [DEGs]) and some bowel dilation. By term, dysregulation was substantial (2,423 DEGs) alongside significant dilation. Normal ontogenetic intestinal maturation patterns were altered, with fewer expected developmental gene changes and discordant pathway regulation. ECM pathway aberrations emerged early and persisted, while ENS, angiogenic, and inflammatory pathways were only dysregulated at term. Fetal repair was associated with normalization of gene expression at term (29 DEGs vs controls). ConclusionIntestinal transcriptional changes in experimental gastroschisis parallel progressive bowel dilation, consistent with a mechanical stress contribution to intestinal injury. Prenatal repair normalizes both dilation and gene expression, indicating a dynamic and potentially modifiable transcriptional program that supports the rationale for early fetal intervention. Mini AbstractIn a fetal ovine model, progressive bowel dilation in gastroschisis parallels transcriptomic dysregulation of ECM remodeling, neurovascular impairment, and inflammation which is normalized by prenatal repair.

developmental biology↗

bioRxiv2026

Proton FLASH preserves neurocognition across delivery techniques: implications for clinical translation in pediatric brain tumors

BackgroundRadiation therapy is integral to the curative treatment of childhood brain tumors but contributes to late neurocognitive impairment in survivors. FLASH (ultra-high dose rate, >40Gy/s) reduces normal-tissue toxicity in preclinical models, and proton-FLASH is currently the only modality capable of delivering ultra-high dose rates to the deep targets, such as pediatric brain tumors. However, two questions remain unresolved before clinical translation: (1) whether the FLASH effect can be achieved on synchrotron-based proton systems, which deliver protons in discrete spills that may be insufficient to cover a clinical target within a single delivery, and (2) which dose-rate metric, among the multiple definitions currently used in the field, best predicts the biological FLASH effect. MethodsC57BL/6 mice (7-8 weeks) received 10 Gy whole-brain RT via a clinical Hitachi ProBEAT synchrotron with CBCT-guided delivery, using three transmission-beam techniques: single-spill pencil beam scanning (SS PBS), multi-spill PBS with [~]2-second inter-spot delay (MS PBS), and passive scatter (PS), compared to conventional (CONV) delivery and unirradiated controls (n=24-28/group, equal sex distribution). Dose rate was quantified using three frameworks: field dose rate (FDR), PBS dose rate (PBSDR), and dose-averaged dose rate (DADR). Recognition memory was assessed by novel object recognition (NOR) at 6 weeks post-RT, and cognitive flexibility was assessed via touchscreen visual discrimination and reversal learning at 14 weeks. Hippocampal neuroinflammation was evaluated by immunofluorescence and immunohistochemistry for Iba1, NeuN, and GFAP. ResultsFLASH conditions were met by SS PBS and PS under all three dose-rate definitions, but MS PBS qualified as FLASH only by DADR. Despite this, neuroprotection was preserved across all three FLASH techniques: discrimination index was significantly higher for SS PBS (P=0.021), MS PBS (P=0.008), and PS (P<0.001) versus CONV, with no significant difference between FLASH techniques. On touchscreen testing, FLASH-treated females demonstrated preserved cognitive flexibility (P=0.047 vs. CONV on reversal learning correct trials). Iba1+ microglia were reduced in FLASH compared to CONV mice, with morphology suggestive of preserved homeostatic state. ConclusionsSynchrotron-based proton FLASH preserves neurocognitive function across all delivery techniques, including under multi-spill delivery essential for treating clinical-scale pediatric brain tumors. Critically, this neuroprotection was observed even for deliveries that qualified as FLASH only by DADR, identifying DADR as the dose-rate metric most relevant to the biological FLASH effect with direct implications for clinical trial design and dose-rate reporting standards.

cancer biology↗

bioRxiv2026

Memory-safe high-performance sequence mapping with rammap

We introduce a reimplementation of the widely used mapping tool minimap2 in Rust called rammap. We demonstrate perfect concordance with minimap2, enabling its backwards compatibility as a drop-in replacement for minimap2-based workflows. Additionally, rammap implements performance optimizations for modern architectures and applications, including AVX512 and WASM v128 SIMD support for dynamic programming alignment and SIMD-accelerated chaining. These achieve comparable or better performance than minimap2 across diverse mapping workloads while maintaining Rusts stronger memory safety constraints. The rammap API exposes both SIMD-accelerated sequence-sequence alignment modules and full mapping pipelines for use as an integrated library. Lastly, we describe the modular architecture and provide examples illustrating the extensibility of major mapping components, including seeding, chaining, and gap-filling/extension to support development of improved or domain-specific mapping components within a high-performance framework.

bioinformatics↗

bioRxiv2026

Sensitive long-read amplicon sequence variant recovery with savont

Long-read amplicon sequencing can profile longer sequences compared to short reads, but recovering amplicon sequence variants (ASVs) is a challenge for long, noisy reads. We present savont, an algorithm for recovering ASVs from modern long-read amplicons with mean accuracy [≥] 98%, including Oxford Nanopore Technologies (ONT) R10.4 and PacBio HiFi reads. Savont requires 5 to 16 times lower sequencing depth for full-length 16S rRNA ONT reads than previous methods and generates up to 95 times more ASVs for complex environments. Savont makes ASV-based analysis from shallow and noisy long-read amplicon sequencing feasible.

bioinformatics↗

bioRxiv2026

Flytrap-Inspired Mesh-Trap Bioelectronics for Full Spherical Electrophysiological Interrogation of 3D Tissues

Three-dimensional (3D) in vitro tissue models are emerging as powerful platforms for studying development, disease, and therapeutic responses, where close monitoring of electrophysiological activity is essential. However, existing probing methods remain limited in accessibility or spatiotemporal resolution for comprehensive electrophysiological mapping of suspended 3D tissues that closely mimic the native environments. Here we introduce a Venus flytrap-inspired bioelectronic mesh system that enables the full spherical enclosure of 3D tissues in a suspended configuration. The system consists of two hemispherical meshes that envelop the tissue, constructed from highly flexible, stretchable, cell-scale ribbons interconnected into a tissue-compliant network with integrated recording electrode arrays. This architecture enables intimate, conformal tissue integration and supports stable electrophysiological recordings over 300 days. The high-resolution recordings allow precise tracking of local dynamics and correlated global signaling, enabling comprehensive assessment of tissue development as well as detailed evaluation of drug responses for disease modeling. Beyond single tissues, the mesh architecture is extended to fully enclose assembloids composed of multiple tissues, enabling characterization of cross-tissue signaling relevant to advanced heterogenous tissue modeling. Furthermore, the system is translated into array-based platforms, demonstrated by a 4x4 array integrating 1024 electrodes, for high-throughput tissue sampling and cross-study analysis. The developed bioelectronic system and integration method provide a broadly applicable platform to advance electrophysiological studies across diverse tissues and organoids.

bioengineering↗

bioRxiv2026

Novel Muscle-Tropic AAV Capsids with Dramatically Enhanced Transduction and Safety Profiles in Non-Human Primates

Adeno-associated virus (AAV) gene therapy holds immense promise for treating muscular dystrophies, yet its efficacy and safety are constrained by the suboptimal tissue tropism of natural serotypes. Here, we employed the REACH platform, which combines rational design and directed evolution, to engineer muscle targeting vectors. Systemic administration in non-human primates (NHPs) revealed that lead candidate M1 mediates a >10-fold increase in skeletal muscle transduction compared to the AAV9 and 2-3 fold higher than MyoAAV, while concurrently achieving a remarkable 183-fold reduction in liver distribution. Furthermore, M1 exhibited significant de-targeting from key off-target tissues, including dorsal root ganglia (11 fold), lung (27 fold), spleen (2 fold), and kidney (2 fold). These findings demonstrate that the REACH platform can generate AAV capsids with simultaneously enhanced muscle tropism and favorable safety profiles, addressing a critical bottleneck in muscle-directed gene therapy.

bioengineering↗

bioRxiv2026

Paving the way for plant-based bioproduction of (Z)-13-octadecenoic moth pheromone compounds

Sex pheromones are eco-friendly agents to control pest insects. Yet, the cost of synthetic pheromone production has restricted their use essentially to high value crops. Plant-based bioproduction of pheromone compounds offers a promising and sustainable alternative, opening up for the deployment of pheromone-mediated pest control also in row crops. The rice leaffolder Cnaphalocrocis medinalis uses C18 pheromone compounds and is a major rice pest in South China. We demonstrate that the fatty acid precursor of the main C18 pheromone component of C. medinalis, (Z)-13-octadecenal, can be biotechnologically produced using the oilseed crop Camelina sativa. First, we used deuterium-labelling to establish an elongation-based pathway for pheromone precursor formation from hexadecanoic (palmitic) acid via desaturation to (Z)-11-hexadecenoic acid and elongation to (Z)-13-octadecenoic acid. Using transient expression in Nicotiana benthamiana, we identified a minimal pathway consisting of a {Delta}11 desaturase (CmedDES1), an elongase (CmedELO1), and a fatty acyl reductase (CmedFAR2) for the heterologous biosynthesis of long-chain pheromone monounsaturated C18 precursors in planta. Co-expression of the insect desaturases CmedDES1 or CsupYPAQ with the Camelina elongase CsaKCS1 in Nicotiana benthamiana resulted in higher production of Z13-18 products compared to co-expression with insect elongases. We finally engineered Camelina sativa seeds through seed-specific co-expression of the Z11-16-forming insect desaturase CsupYPAQ and CsaKCS1 elongase, enabling the accumulation of C18 fatty acid pheromone precursors. Our study paves the way for sustainable production of the sex pheromone of C. medinalis and other C18 monounsaturated pheromone precursors for crop protection.

synthetic biology↗