Biology subjects

Zhang, Q.

Publications and source records attributed to Zhang, Q..

At least 271 records · Page 15Linked to original sources

bioRxiv2024

Motor protein-assisted glycan translocation and sequencing using nanopores

The glycan sequencing remains a significant bottleneck in glycoscience. While nanopore platforms have achieved substantial progress in single-molecule nucleic acid sequencing, their application to glycan sequencing has faced considerable challenges, with limited advancements to date. In this study, we propose a novel strategy for controlling glycan translocation through the MspA nanopore as an initial step toward glycan sequencing. By conjugating the target glycan with a helicase-controlled single-stranded DNA, we successfully achieved sequencing reads of up to eleven glycans. For the first time, we isolated glycan-associated electrical signals, enabling the translocation, stretching, and controlled speed of neutral glycans through the nanopore. This method provides a platform for obtaining glycan read lengths and identifying different glycan modifications, demonstrating the capability to resolve monosaccharide composition and glycosidic linkages. To further improve resolution, we propose engineered M2-MspA to reduce the pore constriction size and enhance precision by minimizing the random thermal motion of the translocating glycan. These modifications are expected to increase the sequencing accuracy and reliability. This work represents the first proof-of-concept demonstration of glycan chain nanopore sequencing and lays a promising foundation for the development of single-molecule glycan fingerprinting and sequencing technologies. We anticipate that this approach will significantly advance the development and commercialization of nanopore-based glycan sequencing techniques.

bioengineering↗

bioRxiv2024

Synthetic ratio computation for programming population composition and multicellular morphology

Recent advancements in genetic engineering have provided diverse tools for artificially synthesizing population diversity in both prokaryotic and eukaryotic systems. However, achieving precise control over the ratios of multiple cell types within a population derived from a single founder remains a significant challenge. In this study, we introduce a suite of recombinase-mediated genetic devices designed to achieve accurate population ratio control, enabling the distribution of distinct functionalities across multiple cell types. We systematically evaluated key parameters influencing recombination efficiency and developed data-driven models to reliably predict binary differentiation outcomes. Using these devices, we implemented parallel and series circuit topologies to create user-defined, complex cell fate branching programs. These branching devices facilitated the autonomous differentiation of precision fermentation consortia from a single founder strain, optimizing cell-type ratios for applications such as pigmentation and cellulose degradation. Beyond biomanufacturing, we engineered multicellular aggregates with genetically encoded morphologies by coordinating self-organization through cell adhesion molecules (CAMs). Our work provides a comprehensive characterization of recombinase-based cell fate branching mechanisms and introduces a novel approach for the bottom-up, high-resolution construction of synthetic consortia and multicellular assemblies.

synthetic biology↗

bioRxiv2024

Ice gliding diatoms establish record-low temperature limit for motility in a eukaryotic cell

Despite periods of permanent darkness and extensive ice coverage in polar environments, photosynthetic ice diatoms display a remarkable capability of living inside the ice matrix. How these organisms navigate such hostile conditions with limited light and extreme cold remains unknown. Using a custom sub-zero temperature microscope during an Arctic expedition, we present the discovery of motility at record-low temperatures in a Eukaryotic cell. By characterizing the gliding motility of several ice diatom species, collected from ice cores in the Chukchi Sea, we record that they retain motility at temperatures as low as -15 {degrees}C. Remarkably, ice diatoms can glide on ice substrates, a capability absent in temperate diatoms of the same genus. This unique ability arises from adaptations in extracellular mucilage that allow ice diatoms to adhere to ice, essential for gliding. Even on glass substrates where both cell types retain motility at freezing temperatures, ice diatoms move an order of magnitude faster, with their optimal motility shifting toward colder temperatures. Combining field and laboratory experiments with thermo-hydrodynamic modeling, we reveal adaptive strategies that enable gliding motility at extreme cold temperatures. These strategies involve increasing internal energy efficiency with minimal changes in heat capacity and activation enthalpy, and reducing external dissipation by minimizing the temperature sensitivity of mucilage viscosity. The discovery of diatoms ice gliding motility opens new routes for understanding their survival within a harsh ecological niche and their migratory responses to rapid environmental changes. Our work highlights the robust adaptability of ice diatoms in one of Earths most extreme settings.

biophysics↗

bioRxiv2024

Multi-purpose controllable protein generation via prompted language models

Deep learning is increasingly powerful for designing proteins that meet structural and functional requirements. However, most existing methods follow a conventional pipeline: first defining a backbone structure and then generating sequences consistent with it. This approach, which encodes all design goals indirectly through structures, restricts flexibility and struggles to address multiple, complex design objectives simultaneously. We present PROPEND, a multi-purpose protein sequence design method based on the "pre-train and prompt" framework. We show PROPENDs broad utility and accuracy both in silico and in vitro by directly controlling multiple properties through the prompt of backbones, blueprints, functional tags, and their combinations. For the five sequences tested with in vitro experiments, PROPEND achieved a maximum functional recovery of 105.2%, significantly outperforming the classical design pipelines 50.8%.

synthetic biology↗

bioRxiv2024

Impact of oral Chlamydia Vaccination on Host Gut Microbiome and Metabolites Composition

Chlamydia trachomatis, an intracellular pathogen, is recognized as the most common sexually transmitted bacterial infection among women worldwide. Chlamydia infections can lead to undesirable clinical outcomes, including pelvic inflammatory disease and infertility. Recently, the gut has been identified as a niche for Chlamydia colonization; however, despite the biological impact on the host remaining under investigation, oral inoculation of Chlamydia as a whole-organism vaccine has been reported as a promising strategy for preventing genital Chlamydia infections. Few studies have evaluated the impact of oral Chlamydia vaccination on the gut microbiome and metabolite changes. In this study, we assessed time-series alterations in the gut microbiome and metabolites following oral Chlamydia inoculation, and we analyzed the composition and correlation between serum immune parameters and the sequencing profiles in the host. We identified 129 microbial changes and 186 significantly different metabolites in the gut across various vaccination approaches during the 30-day immunization process. Additionally, we discussed potential biomarkers of effective immunization based on correlation analysis. IMPORTANCEChlamydia infections primarily lead to morbidity rather than mortality. Consequently, in developing and implementing a Chlamydia vaccine, the utmost priority is ensuring safety. As a promising yet controversial approach, live oral vaccination for Chlamydia raises concerns regarding its impact on the hosts gut environment. Our study not only investigates changes in the gut microbiome and metabolites during vaccination but also identifies potential biomarkers during immunization. These findings are crucial for the development of whole-organism oral Chlamydia vaccines and provide valuable insights into the long-term colonization of Chlamydia in the gut.

microbiology↗

bioRxiv2024

Distinct Binding Modes of Inter-Spike Cross-Linking Suggest a Supplementary Mechanism for SARS-CoV-2 Antibody Neutralization

The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its Omicron subvariants drastically amplifies transmissibility, infectivity, and immune escape, mainly due to their resistance to most neutralizing antibodies. Thus, exploring the mechanisms underlying antibody evasion is crucial. Although the full-length native form of antibody, immunoglobulin G (IgG), offers valuable insights into the neutralization, structural investigations primarily focus on the fragment of antigen-binding (Fab). Here, we employ single-particle cryo-electron microscopy (cryo-EM) to characterize a W328-6H2 antibody, in its native IgG form complexed with severe acute respiratory syndrome (SARS), severe acute respiratory syndrome coronavirus 2 wild-type (WT) and Omicron variant BA.1 spike protein (S). Three high-resolution structures reveal that the full-length IgG forms a centered head-to-head dimer of trimer when bound fully stoichiometrically with both SARS and WT S, while adopting a distinct offset configuration with Omicron BA.1 S. Combined with functional assays, our results suggest that, beyond the binding affinity between the RBD epitope and Fab, the higher-order architectures of S trimer and full-length IgG play an additional role in neutralization, elucidate a potential molecular basis of Omicron immune escape, and expand our understanding on antibody evasion mechanisms.

immunology↗

bioRxiv2024

Phenotypic high-throughput screening identifies modulators of gut microbial choline metabolism

Anaerobic metabolism of dietary choline to trimethylamine (TMA) by the human gut microbiome is a disease-associated pathway. The hosts impaired ability to oxidize TMA to trimethylamine-N-oxide (TMAO) results in trimethylaminuria (TMAU), while elevated serum TMAO levels have been positively correlated with cardiometabolic disease. Small molecule inhibition of gut bacterial choline metabolism attenuates the development of disease in mice, highlighting the therapeutic potential of modulating this metabolism. Inhibitors previously developed to target this pathway are often designed to mimic choline, the substrate of the key TMA-generating enzyme choline trimethylamine-lyase (CutC). Here, we use a growth-based phenotypic high-throughput screen and medicinal chemistry to identify distinct chemical scaffolds that can modulate anaerobic microbial choline metabolism and lower TMAO levels in vivo. These results illustrate the potential of using phenotypic screening to rapidly discover new inhibitors of gut microbial metabolic activities.

microbiology↗

bioRxiv2024

Transcriptome Assembly at Single-Cell Resolution with Beaver

Emerging single-cell RNA sequencing techniques (scRNA-seq) has enabled the study of cellular transcriptome heterogeneity, yet accurate reconstruction of full-length transcripts at single-cell resolution remains challenging due to high dropout rates and sparse coverage. While meta-assembly approaches offer promising solutions by integrating information across multiple cells, current methods struggle to balance consensus assembly with cell-specific transcriptional signatures. Here, we present Beaver, a cell-specific transcript assembler designed for short-read scRNA-seq data. Beaver implements a transcript fragment graph to organize individual assemblies and designs an efficient dynamic programming algorithm that searches for candidate full-length transcripts from the graph. Beaver in-corporates two random forest models trained on 51 meticulously engineered features that accurately estimate the likelihood of each candidate transcript being expressed in individual cells. Our experiments, performed using both real and simulated Smart-seq3 scRNA-seq data, firmly show that Beaver substantially outperforms existing meta-assemblers and single-sample assemblers. At the same level of sensitivity, Beaver achieved 32.0%-64.6%, 13.5%-36.6%, and 9.8%-36.3% higher precision in average compared to meta-assemblers Aletsch, TransMeta, and PsiCLASS, respectively, with similar improvements over single-sample assemblers Scallop2 (10.1%-43.6%) and StringTie2 (24.3%-67.0%). Beaver is freely available at https://github.com/Shao-Group/beaver. Scripts that reproduce the experimental results of this manuscript are available at https://github.com/Shao-Group/beaver-test.

bioinformatics↗

bioRxiv2024

Inhibition of H3K27M-enhanced ATM signaling increases radiation efficacy in diffuse midline glioma

H3K27-altered diffuse midline glioma (DMG) is an aggressive and treatment-resistant form of pediatric high-grade glioma (pHGG). The disease is defined by point mutations in histone H3 that convert lysine 27 to methionine (termed H3K27M), resulting in genome-wide epigenetic changes that drive tumorigenesis. While radiation therapy is the standard of care, subsequent recurrence, often within the high dose radiation field, is universal. We found that the apical DNA damage response (DDR) kinase Ataxia Telangiectasia-Mutated (ATM) was uniquely upregulated in H3K27M-expressing patient tumor samples compared to pHGG expressing only wild-type histone H3. Using a panel of H3K27 isogenic DMG cell lines, we further found that H3K27M was associated with reduced H3K27me3 within the ATM promoter, increased ATM mRNA levels, and elevated DDR signaling, even in the absence of exogenous DNA damage. Consistent with these results, AZD1390, a clinical-grade, CNS-penetrant ATM inhibitor, sensitized H3K27M neurospheres to the long-term effects of radiation on survival, in part due to attenuated repair of radiation-induced DNA damage. Finally, AZD1390 sensitized orthotopic H3K27M mutant tumors to radiotherapy and significantly extended median survival relative to vehicle, AZD1390 or radiation alone (50 days vs 31, 36 or 39 days, respectively) with minimal adverse effects. Taken together, these data provide a direct mechanistic link between the H3K27M mutation and ATM expression and support the clinical investigation of AZD1390 with radiotherapy in H3K27M-altered DMG.

cancer biology↗

bioRxiv2024

Medium-dose irradiation impairs long-term hematopoietic stem cell functionality and hematopoietic recovery to cytotoxic stress

Irradiation and 5-fluorouracil (5-FU) are widely utilized tools in hematopoietic research to generate myeloablation and assess blood recovery dynamics. A comprehensive understanding of their effects on the hematopoietic system is essential for optimizing therapeutic strategies, refining experimental models to modulate hematotoxicity, and interpreting research outcomes. Despite their widespread application, the long-term hematopoietic impacts of irradiation and 5-FU, particularly on hematopoietic stem cells (HSCs), remain incompletely characterized. In this study, we therefore examined the long-term effects of 2 Gy medium-dose ionizing radiation (MDIR) and 150 mg/kg 5-FU on HSCs and the hematopoietic systems resilience to subsequent cytotoxic stress in mice. Our findings demonstrate that MDIR, but not 5-FU, induces sustained impairments in HSC function and results in the selective depletion of MHC class II- HSCs - a subset characterized by high self-renewal potential. Furthermore, MDIR significantly compromised hematopoietic recovery following a subsequent 5-FU challenge, as evidenced by notably reduced platelet and red blood cell (RBC) counts during the critical recovery phase. These findings highlight the distinct and persistent impacts of MDIR and 5-FU on HSCs and hematopoietic function, revealing crucial differences in their mechanisms of action and long-term consequences on the hematopoietic system.

cell biology↗

bioRxiv2024

Aluminium induces suberin biosynthesis in barley roots via ABA

Aluminum (Al) toxicity is a major factor limiting plant growth in acidic soils. The beneficial element silicon (Si) can mitigate some effects of Al. However, the impact of Al on suberized apoplastic barriers in roots are largely unknown while the effects of Si on suberin remains controversial. This study employed physiological, histochemical, and analytical methods, along with Laser Capture Microdissection (LCM) RNA-sequencing, to explore the effects of Al and Si on suberin development in barley (Hordeum vulgare L.), a species sensitive to Al stress. Exposure of barley seedlings to Al resulted in increased suberin deposition, which could be restored with the addition of Si, particularly in the root endodermis. Gene expression analyses using LCM RNA-seq across different root tissues demonstrated that Al-induced suberin biosynthesis is mainly regulated by the abscisic acid (ABA) pathway. In addition, the application of fluridone, an inhibitor of ABA synthesis and a suberin mutant, further supported the pivotal role of ABA in the Al response and the role of suberin in influencing Al uptake. Our findings underscore the complex interplay between Al stress and suberin biosynthesis in barley, providing insights into potential strategies for enhancing crop resilience to Al toxicity.

plant biology↗

bioRxiv2024

Task-irrelevant features in working memory alter current visual processing

AbstractHigher-level cognition depends on visual working memory (VWM), the ability of our brain to maintain and manipulate internal representations of images that are no longer presented to us. An important question in this field is whether VWM is represented in a sensory or nonsensory manner. Progress has been made in understanding the features to be remembered, but the representational nature of the memory-irrelevant features is unclear. Here, we used a dual-task paradigm to investigate how and when the memory-irrelevant features interact with the concurrent visual information. In a series of experiments, participants were asked to perform a visual search task (Experiment 1) or a perceptual discrimination task (Experiments 2 and 3) involving a memory- irrelevant feature while simultaneously holding the other feature for later retrieval. Experiment 1 showed that VWM biases the allocation of attention to color matching to the memory-irrelevant color. More importantly, the degree of VWM-biased attention decreased monotonically with decreasing feature similarity, and this behavioral monotonic gradient profile resembled the tuning curve of feature-selective neurons in the early visual cortex. Experiment 2 revealed that irrelevant features biased ongoing perception, as indicated by the shifted discrimination threshold. Experiment 3 further demonstrated that VWM-biased perception occurs only at short delays but not at prolonged delays. Our results suggest that the memory-irrelevant feature is represented as a sensory analog for a limited period of time in the visual areas where it was initially processed. Our results extend sensory recruitment theory to memory-irrelevant features in VWM.

neuroscience↗

bioRxiv2024

NAD+ - and EVA1-C-dependent reversal of neurological deficits is mediated by differential alternative RNA splicing in tauopathic animal models

Aberrant alternative splicing (ASEs) is an aging hallmark to Alzheimers Disease (AD). Although NAD+ and related metabolites can slow down AD, NAD+ on ASEs in AD remain unclear. Mouse transcriptomic data revealed NR-induced ASEs, focusing on the Eva1-C locus. AI-based algorithms predicted EVA1-C protein structures and protein-protein interactions. AD postmortem brain samples and tauopathy models including transgenic mice and worm was used for validation. NAD+ abundance/metabolic status modulates ASEs and the expression of EVA1-C isoforms, which in turn regulate the interaction with BAG-1 and HSP70 proteins. Importantly, EVA1-C is dramatically reduced in 20 Braak 5/6 AD patients compared to cognitive normal humans in different brain regions. NAD+ metabolism modulates abundance of specific mRNA isoforms, and that ASEs influence disease progression in model tauopathies and potentially AD. These results could facilitate future development of NAD+-based splice-switching therapeutics for AD. TeaserUnveiling the Link Between NAD+ Metabolism and Alzheimers Disease: Discovering the Role of Alternative RNA Splicing in Disease Progression and Potential Therapeutic Targets

neuroscience↗

bioRxiv2024

Adaptive optical correction in in vivo two-photon fluorescence microscopy with neural fields

Adaptive optics (AO) restore ideal imaging performance in complex samples by measuring and correcting optical aberrations, but often require custom-built microscopes with carefully aligned wavefront sensing/shaping devices and can be susceptible to sample motion. Here we describe NeAT, a computational framework using neural fields for AO two-photon fluorescence microscopy. NeAT estimates wavefront aberration and recovers sample structure from a 3D image stack without requiring external datasets for training. Incorporating motion correction in learning and correcting conjugation errors commonly found in commercial microscopes, NeAT is designed for deployment in biological laboratories for in vivo imaging. We validate NeATs performance using a custom-built microscope with a wavefront sensor under varying signal-to-noise ratios, aberration, and motion conditions. With a commercial microscope, we demonstrate real-time aberration correction for in vivo morphological and functional imaging in the living mouse brain, with NeAT improving signal and accuracy of glutamate and calcium imaging of synapses and neurons.

neuroscience↗

bioRxiv2024

S100a4+ alveolar macrophages accelerate the progression of precancerous atypical adenomatous hyperplasia by promoting fatty acid metabolism

Lung cancer is preceded by premalignant lesions, and what factors drive this transformation and the potential regulatory mode in the context of tumor initiation remain to be elucidated. In the course of precancerous lesions, we found a phasic shift in metabolic patterns. Macrophages are a heterogeneous cell population with high plasticity in the tumor microenvironment. Single-cell interaction and metabolic analyses highlighted a cellular state, S100a4+ alveolar macrophages, which exhibited distinct fatty acid metabolic activity, such as palmitic acid metabolism, at the atypical adenomatous hyperplasia stage, accompanied by an angiogenic-promoting function in a pre-neoplastic setting. These findings were reproducible in human single-cell transcriptomes and had been confirmed by histopathological staining and in vitro cell coculture assays. Taken together, the results from this study demonstrated that the S100a4+ alveolar macrophage subset contributes to tumorigenesis by altering its metabolic state, suggesting that metabolic interventions targeting this cell state in the early stage of disease may delay neoplastic transformation of the lung epithelium.

cancer biology↗

bioRxiv2024

Recursive Cleaning for Large-scale Protein Data via Multimodal Learning

AO_SCPLOWBSTRACTC_SCPLOWReliable datasets and high-performance models work together to drive significant advancements in protein representation learning in the era of Artificial Intelligence. The size of protein models and datasets has grown exponentially in recent years. However, the quality of protein knowledge and model training has suffered from the lack of accurate and efficient data annotation and cleaning methods. To address this challenge, we introduce ProtAC, which corrects large Protein datasets with a scalable Automatic Cleaning framework that leverages both sequence and functional information through multimodal learning. To fulfill data cleaning, we propose the Sequence-Annotation Matching (SAM) module in the model, which filters the functional annotations that are more suitable for the corresponding sequences. Our approach is a cyclic process consisting of three stages: first pretraining the model on a large noisy dataset, then finetuning the model on a small manually annotated dataset, and finally cleaning the noisy dataset using the finetuned model. Through multiple rounds of "train-finetune-clean" cycles, we observe progressive improvement in protein function prediction and sequenceannotation matching. As a result, we achieve (1) a state-of-the-art (SOTA) model that outperforms competitors with fewer than 100M parameters, evaluated on multiple function-related downstream tasks, and (2) a cleaned UniRef50 dataset containing [~]50M proteins with well-annotated functions. Performing extensive biological analysis on a cleaned protein dataset, we demonstrate that our model is able to understand the relationships between different functional annotations in proteins and that proposed functional annotation revisions are reasonable.

bioengineering↗

bioRxiv2024

Astrocyte regional specialization is shaped by postnatal development

Astrocytes are an abundant class of glial cells with critical roles in neural circuit assembly and function. Though many studies have uncovered significant molecular distinctions between astrocytes from different brain regions, how this regionalization unfolds over development is not fully understood. We used single-nucleus RNA sequencing to characterize the molecular diversity of brain cells across six developmental stages and four brain regions in the mouse and marmoset brain. Our analysis of over 170,000 single astrocyte nuclei revealed striking regional heterogeneity among astrocytes, particularly between telencephalic and diencephalic regions, at all developmental time points surveyed in both species. At the stages sampled, most of the region patterning was private to astrocytes and not shared with neurons or other glial types. Though astrocytes were already regionally patterned in late embryonic stages, this region-specific astrocyte gene expression signature changed dramatically over postnatal development, and its composition suggests that regional astrocytes further specialize postnatally to support their local neuronal circuits. Across mouse and marmoset, we found hundreds of species differentially expressed genes, as well as divergence in the expression of astrocytic region- and age-differentially expressed genes and the timing of astrocyte maturation relative to birth between the species. Finally, we used expansion microscopy to show that astrocyte morphology is also regionally specialized across cortex, striatum, and thalamus in the mouse.

neuroscience↗

bioRxiv2024

Quantitative proteomic mass spectrometry of protein kinases to determine dynamic heterogeneity of the human kinome

The kinome is a dynamic system of kinases regulating signaling networks in cells and dysfunction of protein kinases contributes to many diseases. Regulation of the protein expression of kinases alters cellular responses to environmental changes and perturbations. We configured a library of 672 proteotypic peptides to quantify >300 kinases in a single LC-MS experiment using ten micrograms protein from human tissues including biopsies. This enables absolute quantitation of kinase protein abundance at attomole-femtomole expression levels, requiring no kinase enrichment and less than ten micrograms of starting protein from flash-frozen and formalin fixed paraffin embedded tissues. Breast cancer biopsies, organoids, and cell lines were analyzed using the SureQuant method, demonstrating the heterogeneity of kinase protein expression across and within breast cancer clinical subtypes. Kinome quantitation was coupled with nanoscale phosphoproteomics, providing a feasible method for novel clinical diagnosis and understanding of patient kinome responses to treatment.

biochemistry↗