Biology subjects

Zhang, P.

Publications and source records attributed to Zhang, P..

At least 19 recordsLinked to original sources

bioRxiv2026

Understanding How Actomyosin Dynamics Drive Apical Constriction by Systematically Tagging and Mapping Actin-Binding Proteins

Apical constriction shapes tissues in fundamental events including gastrulation and neural tube formation. Diverse actin regulators play key roles in shaping cells, but the spatial distribution of most actin regulators in apical constriction is unknown. Here, we describe a systematic approach revealing the endogenous localization of 49 actin regulators in C. elegans gastrulation -- nearly every actin-binding protein (ABP) expressed in the early embryo -- and we use this atlas to test mechanistic hypotheses. We found that many actin regulators localized basolaterally, dependent on the Arp2/3 complex; that linear actin assembly factors enriched apically; and that apically constricting cells had an extra requirement for membrane-cortical linkers present in all cells. These findings answer some key questions about how ABPs function in apical constriction, and they establish a rich resource for investigating actin organization throughout early C. elegans development and a systematic in vivo protein localization reference for the actin cytoskeleton community.

cell biology↗

bioRxiv2026

Physics-informed neural network for predicting myocardial mechanics from in vivo physiological measurements

Structural heart diseases (SHDs) are characterized by progressive myocardial remodeling, yet the tissue-level mechanical properties underlying this process cannot be measured directly in vivo. This limitation restricts the ability of conventional physiological measurements to fully characterize myocardial remodeling and disease progression. Here, we present a physics-informed neural network (PINN) framework that integrates constitutive biomechanics with organ-level physiological measurements to simultaneously infer myocardial biomechanical descriptors and predict physically consistent stress responses. By embedding a hyperelastic constitutive model within the learning process, the framework links physiological measurements with tissue-level mechanics while preserving biomechanical consistency. Using right ventricular remodeling in pulmonary hypertension (PH) as a representative model of SHDs, the proposed framework accurately reproduced nonlinear stress-stretch behavior and outperformed conventional data-driven machine learning approaches for stress prediction. Furthermore, incorporation of PINN-derived tissue-level descriptors with organ-level physiological measurements improved disease stratification and enhanced separation between control, mild, and severe PH remodeling states. These findings support physics-informed constitutive learning as an interpretable framework for integrating organ-level physiology with tissue-level biomechanics and establish a foundation for future biomechanics-informed characterization of myocardial remodeling across SHDs.

bioengineering↗

bioRxiv2026

A microbiota-driven neuroepithelial feed-forward circuit drives gastroesophageal junction tumorigenesis

The gastroesophageal junction (GEJ) is continuously exposed to refluxed bile acids and microbial perturbations, yet how these environmental cues are converted into persistent oncogenic signaling is unknown. Here we show that bile acid remodeling enriches the oral commensal Prevotella melaninogenica at the GEJ, where bacterial succinate activates both vagal sensory neurons and SUCNR1-expressing tuft cells. Activated tuft cells release 15-deoxy-12,14-prostaglandin J2 (15-d-PGJ2), which sensitizes sensory neurons and sustains nerve remodeling, while neuronal CGRP drives expansion and tuft-cell differentiation of neuro-responsive epithelial progenitors through RAMP1. This self-reinforcing microbiota-neuron-epithelium circuit promotes dysplastic progression, and its genetic or pharmacological disruption, including with the approved CGRP antagonist rimegepant, suppresses tumor development, revealing an interceptable mechanism linking environmental dysbiosis to cancer initiation through neural circuits.

cancer biology↗

bioRxiv2026

A claim-centred atlas distinguishes biological corroboration from analytical depth in plant stress transcriptomes

Plant stress transcriptomes are reanalysed far more often than independently replicated, obscuring whether apparent consensus reflects biological corroboration or repeated analysis of the same experiments. Here we present PLEASE (PLant Evidence Atlas for StrEss), a claim-centred atlas that treats the independent experiment, rather than the analysis, as the unit of evidence. PLEASE resolves 88,789 analytical records into 62 dependency-resolved study families. A calibrated core of abiotic and biotic stress programmes persists after dependency collapse. Yet support erodes sharply as claims become more specific. Across stress, organ and cell-lineage contexts, independent-match coverage falls from 1.00 to 0.26 while directional agreement remains near 0.68. Three quarters of sampled contexts contain only one study family. Thus, missing comparable experiments, not pervasive disagreement, is the main barrier to context-specific corroboration. PLEASE separates analytical depth from biological corroboration and pinpoints where independent experiments are most needed.

plant biology↗

bioRxiv2026

Structural basis for phosphorylation-induced inactivation of the rice ammonium transporter AMT1;1

Ammonium (NH4+) uptake and transport in plants are mediated by ammonium transporters (AMTs), which are tightly regulated by phosphorylation to prevent excess ammonium influx and toxic accumulation. However, the mechanism of phosphorylation-mediated inactivation is unique and remains unclear. Here, we report cryo-EM structures of the rice (Oryza sativa) ammonium transporter OsAMT1;1 in its wild-type and phosphomimetic variant T452D states. OsAMT1;1 forms a stable homotrimer, with conserved motifs affirming a shared transport mechanism within the AMT/MEP/Rh superfamily. Our structural analysis reveals that T452D phosphomimetic stabilizes an intracellular salt-bridge network and maintains the channel in a closed state, in which the ICL5 loop positions the hydrophobic plug residue Leu360 near the cytoplasmic exit to occlude the channel exit and abolish complementation capacity. Our findings elucidate phosphorylation-induced inactivation mechanism for the plant AMT1 subfamily, providing a structural paradigm for the post-translational regulation of nutrient uptake.

biophysics↗

bioRxiv2026

A gut-brain microbial sensing pathway mediates host defense and bacterial clearance

The digestive tract is a major site of nutrient absorption. It also harbors the densest microbial communities in our body. It is well known that the brain perceives ingested nutrient information through the intestinal epithelium enteroendocrine cell (EEC)-vagal pathway. Little is known about how the brain senses gut bacteria that reside in the intestinal lumen. In this study, we combined novel in vivo EEC calcium imaging, EEC optochemical stimulation, and vagal sensory neuron calcium imaging in the zebrafish model, and revealed that segregated pathways mediated by different EEC and vagal sensory neuron subtypes differentially perceive beneficial nutrient information and harmful irritant pathogenic bacterial information. Our study revealed that a group of EECs that express the nociceptive receptor Transient receptor potential ankyrin A1 (Trpa1) can be activated by the pathogenic bacterium Edwardsiella tarda (E. tarda) or E. tarda-produced irritant metabolites. These Trpa1+EECs do not sense nutrients. Trpa1+EECs, but not other EECs, uniquely and highly express both Serotonin and the neuronal peptide Pituitary adenylate cyclase-activating polypeptide (Pacap). Using pharmaceutical and genetic approaches, our data showed that Pacap synergizes with Serotonin and is required for Trpa1+EEC-induced vagal activation. Stimulating the Trpa1+EEC-vagal sensory pathway potently inhibits a group of vagal motor neurons that innervate visceral organs in the caudal dorsal motor nucleus of the vagus (cDMV). However, the same group of cDMV neurons is activated by nutrients. Microbially induced cDMV inhibition enhances liver gluconeogenesis and promotes intestinal neutrophil recruitment. Inhibiting glucose metabolism, disrupting Trpa1+EEC-vagal sensory pathway, or optogenetically activating cDMV neurons in E. tarda colonized zebrafish induces intestinal E. tarda to switch from an aggregated phenotype to a diffused phenotype and hinders E. tarda clearance. Furthermore, our data show that disrupting the Trpa1+EEC-vagal sensory pathway impairs intestinal neutrophil recruitment and hinders survival, suggesting a protective role of the Trpa1+EEC-vagal microbial sensing pathway in pathogen defense. Together, our data revealed that a distinct non-nutrient-sensing Trpa1+EEC-vagal circuit senses gut microbial irritants, coordinating neuronal, metabolic, and immune responses to enhance host defense and pathogen clearance.

neuroscience↗

bioRxiv2026

Rational Design of 5' UTRs for Optimized mRNA Expression and Cost-Effective, Rapid Analysis of Capped mRNA

In vitro-transcribed (IVT) messenger RNA (mRNA) therapeutics require rigorous quality control of 5' capping efficiency and 3' poly(A) tail length, both of which constitute critical quality attributes (CQAs). Current analytical workflows for these CQAs rely on hybridization with nucleic acid probes and biotin-based affinity purification, which constrain throughput and increase per-assay cost. Here, we report a rationally designed 5' untranslated region (5' UTR) that sustains high translational efficiency while enabling probe-free, one-step purification for rapid quantification of capping efficiency and poly(A) tail length distribution. This approach exploits a strategically engineered 5' UTR incorporating a purine-only RNase A-resistant fragment terminating at a single pyrimidine cleavage site, together with a translation-enhancing element comprising an N6-methyladenosine (m6A) deposition motif and an 18S rRNA complementarity sequence. This dual-function design accommodates GA-rich sequence segments without compromising mRNA translational output. Compared with conventional probe- and biotin-dependent workflows, the present method substantially reduces cost and processing time and is compatible with simultaneous detection of segmented AmGn poly(A) tail variants. This integrated platform provides a simplified, probe-free and construct-universal for high-throughput in-process control (IPC) of mRNA therapeutics.

bioengineering↗

bioRxiv2026

A Wolbachia pipientis protein confers resistance to virus infection in Drosophila melanogaster

The intracellular bacterium Wolbachia pipientis alters the biology of its arthropod hosts in many ways, and can increase resistance to RNA viruses in both Drosophila and mosquitoes. Wolbachia-induced pathogen blocking has generated much interest because of its potential to restrict insect vector transmission of human diseases caused by RNA viruses. However, the molecular mechanisms by which Wolbachia affects host viral resistance are still mostly elusive. We used dilp2-3,5 mutant Drosophila, which are long-lived, but only in the presence of Wolbachia, to show that the presence of Wolbachia also increased the resistance of the mutant flies to infection with Drosophila C virus (DCV), relative both to mutants lacking Wolbachia and to wild type flies with and without Wolbachia. The insulin mutant flies had higher Wolbachia titres than wild type flies. By RNA-seq analysis of the Wolbachia transcriptome, we identified Wolbachia genes that were more strongly expressed in dilp2-3,5 mutant flies. Ankyrin-domain-containing proteins were among the most strongly up-regulated and they are predicted to be secreted effector proteins. To address their effect on host physiology, we generated 4 transgenic fly lines each with inducible expression of a different genes encoding ankyrin-domain-containing proteins. Expression of 3 of these did not cause obvious effects, but expression of WD0754 at high levels severely shortened fly survival. Interestingly, however, chronic low-level induction of WD0754 increased the resistance of the flies to DCV infection. Proteomics analysis showed a robust, tissue-specific, anti-viral response upon WD0754 induction, and identified the NFkB-like IMD pathway as a potential mediator of the antiviral activity of WD0754. Consistently, WD0754 expression activated Relish, a key downstream transcriptional mediator of IMD signalling, while loss-of Relish blocked the antiviral effect of WD0754. In summary, we identified a Wolbachia-derived ankyrin domain containing protein that modulates host immunity through the IMD pathway.

molecular biology↗

bioRxiv2026

Multi-Omics analysis provides crucial insights into ecological adaptation to dryland of a dominant grass (Psammochloa villosa, Poaceae) in Northwest China

Desertification exerts dramatic selection pressures on the evolution of plants. Despite the key role of ecological adaptation by natural selection to arid grasslands and subsequent intraspecific divergence, specific mechanisms driving this process remain poorly understood. Psammochloa villosa, a perennial forage grass endemic to the arid grasslands in Northwest China, where it thrives in shifting and semi-fixed sand land due to its exceptional drought tolerance, provides an ideal system to study adaptive evolution to aridity. In our study, we assembled a high-quality, chromosome-scale genome and conducted genomic resequencing of 42 populations across its major distribution. The genome assembly, which is approximately 1.55 Gb in size, has a super-scaffold N50 of 66.79 Mb, with 75.84% of the sequences identified as transposable elements. Coalescent phylogeny and genomic collinearity analyses strongly supported that P. villosa and Neotrinia splendens, as the closest taxa, shared a recent whole-genome duplication (WGD) event occurring approximately 18-20 Mya and followed by their divergence around ~11.2 Mya. Based on ancestral grass karyotype (AGK) reconstruction from synteny analysis, our results suggest that, relative to the AGK after the {rho}-WGD event, P. villosa and N. splendens underwent similar chromosomal restructuring and lineage-specific retention of numerous copies, providing a genomic basis for potential ecological adaptation and intraspecific diversification. The expanded XTH family, which encodes enzymes mediating xyloglucan endotransglucosylation and hydrolysis and thereby regulating xyloglucan remodeling, showed strong transcriptional responses under PEG-6000 treatment, suggesting that retained copies may be associated with xerophytic adaptation in P. villosa. Together, these findings suggest that WGD-derived gene retention created a delayed reservoir of genetic diversity that was later shaped by desertification and Qinghai-Xizang Plateau environmental changes, contributing to climate-associated genomic islands and intraspecific differentiation.

genomics↗

bioRxiv2026

MxB N-Terminus Adopts a Stable α-Helix to Engage the HIV-1 Capsid Trimer Interface

The HIV-1 capsid, composed of capsid (CA) proteins arranged into a conical surface lattice, serves as a critical platform for host-pathogen interactions. Many host cofactors regulate HIV-1 infection by selectively recognizing the higher-order CA lattice rather than individual monomers or capsomers. Among these, Myxovirus resistance protein B (MxB) is a key cellular restriction factor that binds the capsid via its N-terminal fragment containing an arginine-rich motif (RRR), blocking HIV-1 infection at early infection stages. However, the structural basis of this interaction has remained elusive. Here, we present a structural characterization of the CA lattice in complex with the MxB N-terminal fragment using cryo-electron tomography and subtomogram averaging. Combining cryoEM structures with EM-guided all-atom molecular dynamics simulations, we identify residue-specific interactions between MxB and the CA trimer interfaces. Notably, residues 10-20 of the MxB N-terminus adopt an alpha-helical conformation that stabilizes binding at the CA trimer interface, revealing a previously unrecognized mode of capsid engagement. These findings provide new insight into arginine-rich motif-mediated recognition by MxB and other host factors and establish a structural framework for the development of capsid-targeting antiviral therapeutics.

microbiology↗

bioRxiv2026

In-cell structural analysis reveals a distinctive chloroplast ribosome in Chlamydomonas reinhardtii

Chloroplast ribosomes synthesize plastid-encoded components of photosynthetic machinery, yet their structure and organization remain poorly understood. We combined cryo-focused ion beam milling, cryo-electron tomography and subtomogram averaging to determine native chloroplast ribosomes in Chlamydomonas reinhardtii. The 4.4-4.9 [A] structure revealed a large arch-like extension on the small subunit (SSU). Comparisons with bacterial and plant chloroplast ribosomes, supported by proteomics, AlphaFold3 predictions and a recent atomic model, indicate that the arch is formed by insertions and extensions in SSU proteins. Classification resolved active, thylakoid-associated ribosomes with density adjacent to the nascent peptide exit and an arch-moved state enriched among thylakoid-associated particles, with coordinated displacement of the arch and beak. Phylogenetic analysis revealed an evolutionary mosaic: the uS3c insertion is broadly distributed across Chlorophyceae, whereas the uS2c insertion, uS5c and PSRP7 are concentrated in Chlamydomonadales, with PSRP7 also in Sphaeropleales. Nuclear-encoded components were recruited stepwise onto a plastid-encoded scaffold, with all four under comparable purifying selection. These findings link a lineage-specific SSU extension to ribosome dynamics, thylakoid association and evolution, highlighting the value of in-cell structural analysis.

plant biology↗

bioRxiv2026

Optimized Kakadu Plum Extracts Inhibit Intracellular Oxidative Stress in Canine Small Intestinal Cell Model

Kakadu plum (Terminalia ferdinandiana), an Australian native fruit, is among the richest known dietary sources of vitamin C and hydrolysable tannins, yet its capacity to protect the intestinal epithelium against oxidative stress remains largely unexplored. This study optimised the extraction of bioactive compounds from freeze-dried Kakadu plum powder and evaluated their antioxidant activity using both chemical and cellular antioxidant in vitro assay. Phenolic compounds were extracted using three solvents (water, 80% ethanol, and 80% methanol) combined with shaking, ultrasound, or microwave assistance. Solvent, rather than processing technique, was the dominant determinant of antioxidant capacity: ethanol and methanol maximised total phenolic content, total flavonoid content, and DPPH radical-scavenging activity, whereas water extracts showed the highest ferric-reducing antioxidant power. Twenty-four phenolic compounds identified by HPLC-ESI-QTOF-MS/MS were mapped by network pharmacology to nine core oxidative-stress targets, and cross-species molecular docking predicted conserved binding of key phenolics to canine orthologs of PTGS2 and MMP2. In an H2O2-induced oxidative-stress in vitro cell model using canine small intestinal epithelial cells, both water (less than 25 ug/mL) and ethanol (less than 250 ug/mL) extracts significantly suppressed intracellular reactive oxygen species (ROS) in a dose-dependent manner, with the ethanol extract effective across a wider concentration range. This work demonstrated that Kakadu plum extract could be a promising natural, multi-target antioxidant ingredient for canine intestinal health, and provided a reference for future in vivo research.

biochemistry↗

bioRxiv2026

In situ Discovery of Immune Repertoire Reveals Antitumor Immunity and Therapeutic Antibodies

Spatial transcriptomics offers a glimpse into the immunology of tissues. However, limitations in spatial transcriptomics preclude the detection of highly diverse, low-abundance, and previously unknown sequences, including immune repertoires and microbiota. Here, we introduce Archimap, a spatial transcriptomic platform that simultaneously profiles spatial transcriptomes, immune repertoires, and microbiota from formalin-fixed paraffin-embedded (FFPE) tissues. Using Archimap, we profile the spatial localization of TCRs, BCRs, and the microbiota landscape in archived clinical tissues at single-cell resolution. Through comprehensive benchmarking, we validate Archimaps performance and fidelity. Archimap in situ assembles the immune complex and reconstructs the clonal evolution of antibodies. Together, Archimap shows the power of in situ discovery of functional immune repertoires for their antitumor immunity.

bioinformatics↗

bioRxiv2026

Myeloid-targeted RNA nanotherapeutics rewire cholesterol metabolism to unleash anti-tumor immunity in glioblastoma

Tumor-associated myeloid cells (TAMCs) dominate the glioblastoma (GBM) microenvironment and suppress anti-tumor immunity. Here, we identify cholesterol efflux via ABCA1 as a targetable metabolic checkpoint controlling TAMC immunosuppression in GBM. Reprogramming TAMC cholesterol metabolism using TAMC-targeting lipid nanoparticle encapsulating ABCA1 siRNA (ABCA1 LNP) converts TAMCs into potent antigen-presenting cells with enhanced pro-inflammatory activity and antigen-presenting capacity, thereby inducing T cell activation, expansion, and tumor infiltration. Mechanistically, ABCA1 blockade induces cholesterol accumulation in TAMC membranes, promoting lipid raft formation and enhancing MHC-I-mediated antigen presentation. In multiple preclinical GBM models, ABCA1 LNP treatment dramatically induces T cell priming, extends animal survival, and overcomes GBM resistance to radiotherapy and immune checkpoint therapy. This efficacy was well-maintained in stem-like and recurrent GBM models, GBM patient specimens, and a renal cell carcinoma model. Altogether, our work identifies cholesterol efflux as a targetable metabolic vulnerability in TAMCs to overcome therapy resistance in myeloid-rich, immunologically "cold" tumors.

immunology↗

bioRxiv2026

HPAI H5N1 risk in Australia: a model for the prediction of poultry outbreaks

The panzootic highly pathogenic avian influenza (HPAI) H5N1 virus has now been detected on the Australian mainland, with incursions from the sub-Antarctic region posing an increasing threat to domestic wildlife and poultry populations. Our study aimed to predict the risk of HPAI H5N1 poultry outbreaks across Australia at the local government area (LGA) level using a range of influential risk factors. We first used a Maximum Entropy (MaxEnt) model to estimate the environmental suitability for HPAI H5N1 occurrence across Australia. The resulting suitability layer was then integrated with five additional predictor layers, including abundance data for two Southern Ocean wild birds, one of which has introduced HPAI H5N1 into Australia; abundance data for 28 native Australian wild birds; native bird flyways across Australia; Australian chicken density; and poultry farm density. The six layers were aggregated and averaged to generate an HPAI H5N1 risk map for poultry outbreaks across Australian LGAs. Although most incursions have occurred in Western Australia (WA) and South Australia (SA), we identified New South Wales (NSW) and Victoria (VIC) as having the highest predicted risk of HPAI H5N1 poultry outbreaks. Additional high-risk areas were identified in WA, SA, and Tasmania (TAS). In contrast, the Northern Territory (NT) and large parts of Queensland (QLD), WA, and SA were predicted to be at low risk. These findings provide a spatially explicit framework to support targeted surveillance, preparedness, and biosecurity measures aimed at mitigating the impact of future HPAI H5N1 outbreaks in Australian poultry.

bioinformatics↗

bioRxiv2026

Quantitative Comparison of 3D-1D Vascular Coupling Models: Lateral Average versus Sphere of Influence Methods

Computational models coupling one-dimensional vascular networks with three-dimensional tissue domains are widely used for predicting blood flow distribution in tumor perfusion, drug delivery, and therapeutic planning. Two prominent coupling paradigms have emerged: the Lateral Average Model (LAM) which implements distributed transmural exchange via a vessel wall conductivity parameter{gamma} (m Pa-1 s-1), and the Sphere of Influence (SOI) model, which employs localized terminal coupling via a source sphere radius{varepsilon} (m). Despite their broad application, systematic quantitative comparisons of their parametric behavior and predictive equivalence remain lacking. We compare LAM and SOI in 3D-1D simulations on a benchmark vascular network and a porcine liver study with a hepatic arterial network reconstructed from CT arteriography. Across a benchmark vascular network under three sink configurations, the LAM net flow rate rose smoothly with{gamma} and saturated at a plateau, while the SOI net flow rate increased with{varepsilon} without saturating; as a result, global-flow equivalence between the two formulations exists only for particular boundary geometries, and not at all within the tested parameter range for one of the three configurations examined. Despite this partial agreement in total flow, the two models diverged substantially in regional perfusion: in a porcine hepatic arterial network reconstructed from CT arteriography, SOI predicted stable perfusion fractions to two regions of interest across its full tested parameter range, whereas LAM predictions for the same regions varied several-fold with vessel wall permeability and, at low permeability, could invert which region received more flow. These results indicate that the choice of coupling model has limited consequence for predicted total organ flow but substantial consequence for predicted local drug delivery, and we provide guidance for selecting between the two formulations depending on the clinical or research question being asked. Author SummaryWhen doctors plan treatments for liver cancer, they often rely on computer simulations to predict how blood flows through the liver and how well a drug will reach the tumor. These simulations depend on mathematical models that describe how blood moves from vessels into surrounding tissue. Two commonly used approaches exist for building these models, but researchers have generally chosen between them based on habit or convenience rather than on a principled understanding of how their predictions differ. In this work, we directly compared these two approaches, one that spreads blood exchange continuously along the vessel wall, and one that delivers blood from the vessel tips into a surrounding spherical zone, using both a simple test network and a realistic pig liver reconstructed from medical imaging. We found that the two approaches can agree on the total amount of blood reaching the liver, but disagree substantially on where that blood goes within the tissue. This distinction matters enormously for treatment planning: a model that predicts the right total blood flow but delivers it to the wrong region of the liver could lead to an inaccurate forecast of drug concentration at the tumor site. Our results provide practical guidance for researchers on which approach to use depending on what information is available and what question is being asked.

biophysics↗

bioRxiv2026

Targeting cellular senescence alleviates bone marrow aging

Aging of the hematopoietic system impairs hematopoietic stem cell (HSC) function and alters bone marrow niche behavior, increasing susceptibility to anemia, infections, and hematologic malignancies. Here, pharmacologic clearance of senescent cells with the PROTAC compound 753b simultaneously targeting BCL-xL and BCL-2 reverses key secretory, transcriptional, and functional hallmarks of hematopoietic aging with low toxicity, restoring balanced lineage output. Single-cell RNA sequencing further demonstrates that 753b treatment attenuates aging-associated transcriptional signatures in HSCs, while selectively eliminating senescent, pro-survival niche cells without grossly perturbing niche composition. Functionally, 753b suppresses pro-inflammatory cues from both niche and hematopoietic cells including those emanating from neutrophil progenitors, rebalancing global bone marrow secretory ecosystem across stromal and hematopoietic compartments. Collectively, we identify 753b-induced senescent cell clearance as a powerful strategy to rejuvenate aged hematopoiesis and re-establish homeostatic communication between HSCs and their microenvironment, with implications for mitigating age-related hematologic dysfunction and improving hematologic health in older individuals.

cell biology↗

bioRxiv2026

Quinoa: Efficient and Robust CTF Estimation for CryoET Tilt Series

Accurate estimation of the contrast transfer function (CTF) of tilt images is a critical first step in cryo electron tomography (cryoET), enabling reliable recovery of high-resolution structural information from thick, heterogeneous specimens. This challenge is especially acute in in situ cryoET, where macromolecules are imaged in their native cellular environment, often at high tilt and through substantial specimen thickness, with correspondingly low signal-to-noise ratios. Although CTF parameters can be later refined using reference-based approaches, accurate initial estimates are critical for downstream processing and the interpretability of tomographic reconstructions, yet they remain difficult to automate. Here, we present Quinoa, a software package designed to address these challenges. Quinoa first validates the tilt geometry and assesses data quality to generate robust initial estimates of defocus and phase shift. These estimates are then refined through optimization of a single global model, enabling precise fitting of the per-image defoci, tilt-dependent astigmatisms, time-dependent phase shifts, the specimen orientation (rotation, tilt and pitch) and the specimen thickness. Notably, and as a key distinguishing feature of this approach is that Quinoa fits equiphase-binned polar power spectra. This substantially reduces the computational cost of optimization without sacrificing accuracy, enabling more progressive and exhaustive refinement passes that further improve robustness. We validated Quinoa using both simulated and experimental data and benchmarked its performance against Warp, Ctfplotter, CTFMeasure, and AreTomo. Our results show that Quinoa is the most robust approach across all simulated cases, maintaining high accuracy even in the simultaneous presence of severe astigmatism, high specimen inclination and variable phase shift. Integrated recovery mechanisms further allow Quinoa to adapt automatically to a wide range of pixel sizes, defoci, astigmatisms and specimen thicknesses. Despite fitting a more complex and dynamic model, Quinoa remains extremely efficient due to extensive GPU acceleration, making it well suited for real-time monitoring during data collection as well as high-throughput offline batch processing. By improving automated CTF estimation in challenging tomographic data, Quinoa supports more accurate structural analysis of cells and tissues in situ.

biophysics↗