Biology subjects

Quan, Q.

Publications and source records attributed to Quan, Q..

4 recordsLinked to original sources

bioRxiv2026

Nanoneedle-Enabled Quantification of rAAV9 Capsid and Genome Integrity Reveals a Truncation Hotspot Locus in a 4.5 kb Transgene

BackgroundAdeno-associated virus (AAV) vectors are foundational to gene therapy but remain difficult to manufacture at high quality. Vector preparations frequently contain empty capsids and truncated genomes, diminishing potency and increasing immunogenic and production burdens. Conventional assays such as qPCR and ddPCR quantify only short regions, overestimating functional genomes and failing to resolve truncation patterns. MethodsWe applied the NanoMosaic Tessie nanoneedle platform to quantify AAV9 capsid and genome titers, directly distinguishing full-length (>4 kb) and truncated genomes. A 4.5 kb CAG- Luciferase-WPRE-bGH transgene packaged in AAV9 was analyzed using (i) nanoneedle "Probe Walk" assays to map truncations, (ii) PacBio SMRT long-read sequencing for orthogonal validation, and (iii) sedimentation velocity analytical ultracentrifugation (SV-AUC) to assess particle heterogeneity. ResultsProbe-walk mapping revealed asymmetric packaging with a [~]570 bp truncation hotspot 0.44-1.01 kb from the left inverted terminal repeat (ITR). PacBio sequencing confirmed positional concordance, identifying left partial reads clustering within the same region. SV-AUC resolved four major populations--empty (1.8%), partial (4.6%), full-length (70.4%), and high-molecular-weight (HMW) species (18.5%)--suggesting dimeric or multimeric capsids co-sedimenting with full-genome particles. Discussion and ConclusionsThe nanoneedle platform provided quantitative, region-specific insights into genome integrity that aligned with sequencing data while requiring minimal sample and processing time. The disproportion between molecular and AUC estimates indicates that apparent "full" species may contain long partial genomes or multimeric capsids bearing partial genomes. Together, these results establish the NanoMosaic Tessie system as a critical quality attribute (CQA) tool for assessing genome integrity and guiding process optimization. Integrating nanoneedle-based analytics early in development enables detection of truncation hotspots, improvement of vector fidelity, and acceleration of scalable, high-quality AAV manufacturing.

molecular biology↗

bioRxiv2025

CNS-Tau Specific Antibodies Illuminate Disease Signatures Across Tauopathies

BackgroundAlternative splicing of the MAPT gene produces distinct tau isoforms in the central and peripheral nervous systems (CNS and PNS), yet their respective biological and pathological roles remain poorly understood. Recent studies suggest that CNS-tau may play a key role in amyloid-{beta} associated neurodegeneration in Alzheimers disease (AD), but the absence of isoform-specific tools has limited both mechanistic insight and biomarker development. We aimed to develop and validate CNS-tau-specific monoclonal antibodies and assess their utility in neuropathology and fluid-based biomarker assays across AD and primary tauopathies. MethodsWe generated six recombinant rabbit monoclonal antibodies targeting a CNS-tau-specific sequence encoded by exons 4 and 5. Specificity and affinity were evaluated via biolayer interferometry, immunoblotting, and tau-expressing HEK293 models. The lead clone, LL-T-1-1, was tested in postmortem brain sections from AD (n = 23), progressive supranuclear palsy (PSP, n = 3), and corticobasal degeneration (CBD, n = 3). A second clone, LL-T-1-5, was optimized for use in plasma assays via an ultrasensitive nanoneedle platform, LoD < 1 pg/ml. ResultsLL-T-1-1 showed nanomolar affinity for CNS-tau and no cross-reactivity with PNS-tau. It selectively labeled dystrophic neurites in AD and all hallmark tau lesions in PSP and CBD without antigen retrieval. LL-T-1-5-based plasma assays revealed CNS-tau levels significantly correlated with cognitive scores (MMSE and QDRS) and differentiated impaired from unimpaired individuals. ConclusionsCNS-tau-specific antibodies LL-T-1-1 and LL-T-1-5 provide new tools for neuropathology and fluid biomarker development across tauopathies.

neuroscience↗

bioRxiv2024

Deep generalizable prediction of RNA secondary structure via base pair motif energy

Deep learning methods have demonstrated great performance for RNA secondary structure prediction. However, generalizability is a common unsolved issue on unseen out-of-distribution RNA families, which hinders further improvement of the accuracy and robustness of deep learning methods. Here we construct a base pair motif library that enumerates the complete space of the locally adjacent three-neighbor base pair and records the thermodynamic energy of corresponding base pair motifs through de novo modeling of tertiary structures, and we further develop a deep learning approach for RNA secondary structure prediction, named BPfold, which learns relationship between RNA sequence and the energy map of base pair motif. Experiments on sequence-wise and family-wise datasets have demonstrated the great superiority of BPfold compared to other state-of-the-art approaches in accuracy and generalizability. We hope this work contributes to integrating physical priors and deep learning methods for the further discovery of RNA structures and functionalities.

bioinformatics↗

bioRxiv2018

Effects of planting density on the growth and photosynthetic characteristics of Alternanthera philoxeroides under different nutrient conditions

Density and nutrient level are important factors that might affect the growth of invasive plants. To reveal the effects of plant density on the performance of invasive plant Alternanthera philoxeroides under different nutrient conditions, a greenhouse experiment was conducted in which A. philoxeroides was planted at three densities (low, medium and high) under three nutrient levels (low, medium and high). The results showed that both planting density and nutrient levels had significant effects on the growth of the plant. The biomass of individual plant and all plants in one pot under medium nutrient level were the highest while the photosynthetic rate and total chlorophyll content were the highest at the high nutrient level. Under different nutrient levels, the photosynthetic rate was the highest at medium planting density. The biomass of single plant decreased with the increase of population density, while the total biomass in the whole pot increased with the increase of density. These characteristics might contribute to the invasion of A. philoxeroides and help the plant to form monodominant community.

plant biology↗