Biology subjects

Qian, L.

Publications and source records attributed to Qian, L..

At least 37 records · Page 2Linked to original sources

bioRxiv2024

A 3D Image Segmentation Study of U-Net on CT Images of the Human Aorta with Morphologically Diverse Anatomy

For the machine learning -assisted diagnosis of cardiac diseases, such as thoracic aortic aneurysm, the geometries of the heart and blood vessels need to be reconstructed from medical images, which is usually done by image segmentation followed by meshing. In this study, we applied U-Net (2D and 3D versions), a deep neural network with a U-shaped architecture, to segment human aorta from CT images. From our experiments, we have the following observations: (1) 2D U-Net, which segments each of the 2D slices of a 3D CT image independently, produced erroneous fragments (e.g., missing part of the aorta) and boundaries (i.e., aortic walls) in 3D; (2) 3D U-Net, which does segmentation in 3D regions of a 3D CT image, performed much better than 2D U-Net. We also observe the major weakness of the 3D U-Net: the reconstructed geometries of the aortic wall had large errors (measured by HD95) for some cases. The 3D U-Net in this study serves as a baseline for developing more advanced architectures of deep neural networks for more accurate geometry reconstruction of human aorta.

bioengineering↗

bioRxiv2024

Cholinergic basal forebrain neurons regulate vascular dynamics and cerebrospinal fluid flux

Waste from the brain is cleared via a cerebrospinal fluid (CSF) exchange pathway, the dysfunction of which is suggested to underlie the pathogenesis of many brain conditions. Coherent cerebrovascular oscillation that couples with pulsatile CSF inflow is suggested to drive the fluid flux. However, how this coupling is regulated, whether it mediates waste clearance, and why fluid flux is impaired in disease status remain unclear. Here we show that vascular-CSF coupling correlates with cortical cholinergic activity in non-demented aged humans. The causal role of basal forebrain cholinergic neurons that project to the cortex is then verified by specific lesioning in mice, revealing correlated changes in vascular-CSF coupling, arterial pulsation and glymphatic flux, which can be altered by an acetylcholinesterase inhibitor. These results suggest a neurovascular mechanism by which CSF/glymphatic flux is modulated by cholinergic neuronal activity, thereby providing a conceptual basis for the development of diagnostics and treatments for glymphatic dysfunction.

neuroscience↗

bioRxiv2024

MIRO1 controls energy production and proliferation of smooth muscle cells

BackgroundThe outer mitochondrial Rho GTPase 1, MIRO1, mediates mitochondrial motility within cells, but implications for vascular smooth muscle cell (VSMC) physiology and its roles in vascular diseases, such as neointima formation following vascular injury are widely unknown. MethodsCarotid ligation was performed in an in vivo model of selective Miro1 deletion in smooth muscle cells. VSMC proliferation during the cell cycle and molecular mechanisms of smooth muscle cell proliferation were explored in cultured aortic VSMCs by imaging mitochondrial positioning and cristae structure and assessing the effects on ATP production, metabolic function, and interactions with components of the electron transport chain (ETC). MIRO1 expression was also analyzed in human coronary arteries, and its function was assessed via knockdown in human coronary artery VSMCs. ResultsMIRO1 was highly expressed in VSMCs within human atherosclerotic plaques. MIRO1 facilitated VSMC proliferation and neointima formation by regulating mitochondrial positioning and PDGF-stimulated ATP production and respiration, critical for cell-cycle progression at G1/S. Deletion of Miro1 disrupted mitochondrial cristae structure, diminished ETC complex I activity, and impaired supercomplex formation. Notably, restoring MIRO1 function with expression of wild type MIRO1 recovered proliferation and ATP production and respiration, whereas a mutant lacking EF hands, which are essential for mitochondrial motility, only partially rescued these effects. MIRO1 knockdown in human coronary artery VSMCs confirmed its pivotal role in mitochondrial function and VSMC proliferation. ConclusionsThis study highlights two key mechanisms by which MIRO1 regulates VSMC proliferation. First, it maintains ATP synthesis by preserving mitochondrial cristae integrity. Second, its Ca2+-dependent EF hands enable ATP-dependent mitochondrial positioning. By linking mitochondrial motility and energy production to VSMC physiology, these findings position MIRO1 as a critical regulator of vascular remodeling and a potential target for therapeutic interventions.

cell biology↗

bioRxiv2024

TurboID-mediated surface protein biotinylation to inhibit the growth of Staphylococcus aureus

Staphylococcus aureus (S. aureus) infection is major cause of nosocomial infections. Antibiotic treatment for S. aureus remains the primary solution for managing S. aureus infections, which, however, increases the risk of antibiotic resistance. To broaden the resolutions on S. aureus infection, here we report TurboID-mediated protein proximity technologies to inhibit the growth of S. aureus. To achieve this goal, we utilized synthetic biology techniques to create a fusion protein named N-AgrD-TurboID (Agr-ID). The N-AgrD domain includes auto-inducer peptide (AIP) which combined to the surface AgrC protein on S. aureus. As such, TurboID then catalyzed the production of biotinoyl-5-AMP anhydride, triggering the biotinylation of surface proteins on S. aureus 25923 which were visualized by using fluorescence microscopy after incubating with Alexa Fluor 647-conjugated streptavidin. The biotinylation of surface protein on S. aureus 25923, S. aureus 43300, and S. aureus 6538 (MRSA) also resulted in growth inhibition and impaired colonization. Moreover, the biotinylation on surface protein further inhibited virulence protein production in S. aureus 25923, as indicated by reduced apoptosis of HEK 293T cells after treatment with S. aureus 25923 lysates. Overall, our work reveals that the biotinylation of surface proteins can inhibit the growth and toxicity of S. aureus 25923, S. aureus 43300, and S. aureus 6538 (MRSA), indicating therapeutic potential in clinical treatment.

microbiology↗

bioRxiv2024

A Rigorous Multi-Laboratory Study of Known PDAC Biomarkers Identifies Increased Sensitivity and Specificity Over CA19-9 Alone

A blood test that enables surveillance for early-stage pancreatic ductal adenocarcinoma (PDAC) is an urgent need. Independent laboratories have reported PDAC biomarkers that could improve biomarker performance over CA19-9 alone, but the performance of the previously reported biomarkers in combination is not known. Therefore, we conducted a coordinated case/control study across multiple laboratories using common sets of blinded training and validation samples (132 and 295 plasma samples, respectively) from PDAC patients and non-PDAC control subjects representing conditions under which surveillance occurs. We analyzed the training set to identify candidate biomarker combination panels using biomarkers across laboratories, and we applied the fixed panels to the validation set. The panels identified in the training set, CA19-9 with CA199.STRA, LRG1, TIMP-1, TGM2, THSP2, ANG, and MUC16.STRA, achieved consistent performance in the validation set. The panel of CA19-9 with the glycan biomarker CA199.STRA improved sensitivity from 0.44 with 0.98 specificity for CA19-9 alone to 0.71 with 0.98 specificity (p < 0.001, 1000-fold bootstrap). Similarly, CA19-9 combined with the protein biomarker LRG1 and CA199.STRA improved specificity from 0.16 with 0.94 sensitivity for CA19-9 to 0.65 with 0.89 sensitivity (p < 0.001, 1000-fold bootstrap). We further validated significantly improved performance using biomarker panels that did not include CA19-9. This study establishes the effectiveness of a coordinated study of previously discovered biomarkers and identified panels of those biomarkers that significantly increased the sensitivity and specificity of early-stage PDAC detection in a rigorous validation trial.

cancer biology↗

bioRxiv2024

Evaluation of Deep Neural Network Models for Instance Segmentation of Lumbar Spine MRI

Intervertebral disc disease, a prevalent ailment, frequently leads to intermittent or persistent low back pain, and diagnosing and assessing of this disease rely on accurate measurement of vertebral bone and intervertebral disc geometries from lumbar MR images. Deep neural network (DNN) models may assist clinicians with more efficient image segmentation of individual instances (discs and vertebrae) of the lumbar spine in an automated way, which is termed as instance image segmentation. In this work, we evaluated 15 existing DNN models for lumbar spine MR image segmentation. We introduced a new data augmentation technique to create synthetic yet realistic MR image dataset, named SSMSpine, which is made publicly available. The 15 image segmentation models are evaluated on our private in-house dataset and the public SSMSpine dataset, using two metrics, Dice Similarity Coefficient and 95% Hausdorff Distance. The SSMSpine dataset are available at https://github.com/jiasongchen/SSMSpine.

bioengineering↗

bioRxiv2024

FECDO-Flexible and Efficient Coding for DNA Odyssey

DNA has been pursued as a compelling medium for digital data storage during the past decade. While large-scale data storage and random access have been achieved in artificial DNA, the synthesis cost keeps hindering DNA data storage from popularizing into daily life. In this study, we proposed a more efficient paradigm for digital data compressing to DNA, while excluding arbitrary sequence constraints. Both standalone neural networks and pre-trained language models were used to extract the intrinsic patterns of data, and generated probabilistic portrayal, which was then transformed into constraint-free nucleotide sequences with a hierarchical finite state machine. Utilizing these methods, a 12%-26% improvement of compression ratio was realized for various data, which directly translated to up to 26% reduction in DNA synthesis cost. Combined with the progress in DNA synthesis, our methods are expected to facilitate the realization of practical DNA data storage.

bioinformatics↗

bioRxiv2024

The role of prospective contingency in the control of behavior and dopamine signals during associative learning

Associative learning depends on contingency, the degree to which a stimulus predicts an outcome. Despite its importance, the neural mechanisms linking contingency to behavior remain elusive. Here we examined the dopamine activity in the ventral striatum - a signal implicated in associative learning - in a Pavlovian contingency degradation task in mice. We show that both anticipatory licking and dopamine responses to a conditioned stimulus decreased when additional rewards were delivered uncued, but remained unchanged if additional rewards were cued. These results conflict with contingency-based accounts using a traditional definition of contingency or a novel causal learning model (ANCCR), but can be explained by temporal difference (TD) learning models equipped with an appropriate inter-trial-interval (ITI) state representation. Recurrent neural networks trained within a TD framework develop state representations like our best handcrafted model. Our findings suggest that the TD error can be a measure that describes both contingency and dopaminergic activity.

neuroscience↗

bioRxiv2023

Parallel Molecular Data Storage by Printing Epigenetic Bits on DNA

DNA storage has shown potential to transcend current silicon-based data storage technologies in storage density, lifetime and energy consumption. However, writing large-scale data directly into DNA sequences by de novo synthesis remains uneconomical in time and cost. Inspired by the natural genomic modifications, in this work, we report an alternative, parallel strategy that enables the writing of arbitrary data on DNA using premade nucleic acids. With epigenetic modifications as information bits, our system employed DNA self-assembly guided enzymatic methylation to perform movable-type printing on universal DNA templates. By programming with a finite set of 700 DNA movable types and 5 templates, we achieved the synthesis-free writing of [~]270000 bits on an automated platform with 350 bits written per reaction. The data encoded in complex epigenetic patterns were retrieved high-throughput by nanopore sequencing, and algorithms were developed to finely resolve 240 modification patterns per sequencing reaction. Our framework presents a new modality of DNA-based data storage that is parallel, programmable, stable and scalable. Such a modality opens up avenues towards practical data storage and dual-mode data functions in biomolecular systems.

biochemistry↗

bioRxiv2023

Fatty acid synthesis promotes inflammasome activation through NLRP3 palmitoylation.

Inflammasomes are multi-protein complexes assembled by NOD-like receptor (NLR) family of proteins, which play critical roles in infectious, inflammatory and metabolic diseases. The assembly of the NLRP3 inflammasome is triggered upon recognition of an apt stimulus by the sensor protein, resulting in binding to pro-caspase-1 via the adaptor protein ASC. Inflammasome activation results in the maturation of the precursor forms of cytokines IL-1{beta} and IL-18, along with caspase-1-dependent pyroptosis, a pro-inflammatory form of cell death. Emerging evidence suggests the involvement of lipid metabolism in inflammasome activation; however, the precise mechanisms by which lipids regulate the NLRP3 inflammasome remain ambiguous. A multi-enzyme protein, fatty acid synthase (FASN) is a central regulator of lipid metabolism partaking an essential role in fatty acid biosynthesis pathway by catalysing the production of palmitic acid. Palmitic acid acts as a precursor to long-chain fatty acids and additionally regulates cellular functions by palmitoylation, a process in which palmitate is reversibly added to cysteine residues of target proteins, modifying protein localization and function. Here, we undertook a pharmacological approach to investigate the roles of fatty acid biosynthetic pathway in NLRP3 inflammasome activation. Our results demonstrated that inhibition of FASN in primary mouse and human macrophages abrogates the activation of the NLRP3 inflammasome, resulting in blunted caspase-1 activation. Furthermore, this phenomenon relied on protein palmitoylation as in vitro and in vivo abrogation of palmitoylation similarly reduced NLRP3 activation, which could be restored by exogenously supplementing palmitate in cultured cells. Consequently, an acyl biotin exchange assay corroborated NLRP3 palmitoylation. Notably, activation of the dsDNA sensing AIM2 inflammasome remained unaltered when either FASN or palmitoylation was blocked. These results therefore highlight the pivotal role of FASN and palmitoylation, shedding new mechanistic insights into the activation of the NLRP3 inflammasome.

immunology↗

bioRxiv2023

SARS-CoV-2 spike protein induces the cytokine release syndrome by stimulating T cells to produce more IL-2

Cytokine release syndrome (CRS) is one of the leading causes of mortality in COVID-19 patients caused by the SARS-CoV-2 coronavirus. However, the mechanism of CRS induced by SARS-CoV-2 is vague. This study shows that dendritic cells loaded with spike protein of SARS-CoV-2 stimulate T cells to release much more IL-2, which subsequently cooperates with spike protein to facilitate peripheral blood mononuclear cells to release IL-1{beta}, IL-6, and IL-8. These effects are achieved via IL-2 stimulation of NK cells to release TNF- and IFN-{gamma}, as well as T cells to release IFN-{gamma}. Mechanistically, IFN-{gamma} and TNF- enhance the transcription of CD40, and the interaction of CD40 and its ligand stabilizes the membrane expression of TLR4 which serves as a receptor of spike protein on the surface of monocytes. As a result, there is a constant interaction between spike protein and TLR4, leading to continuous activation of NF-{kappa}B. Furthermore, TNF- also activates NF-{kappa}B signaling in monocytes, which further cooperates with IFN-{gamma} and spike protein to modulate NF-{kappa}B-dependent transcription of CRS-related inflammatory cytokines. Targeting TNF-/IFN-{gamma} in combination with TLR4 may represent a promising therapeutic approach for alleviating CRS in individuals with COVID-19.

immunology↗

bioRxiv2023

SIDERITE: Unveiling Hidden Siderophore Diversity in the Chemical Space Through Digital Exploration

Siderophores, a highly diverse family of secondary metabolites, play a crucial role in facilitating the acquisition of the essential iron. However, the current discovery of siderophore relies largely on manual approaches. In this work, we introduced SIDERTE, a digitized siderophore information database containing 872 siderophore records with 649 unique structures. Leveraging this digitalized dataset, we gained a systematic overview of siderophores by their clustering patterns in the chemical space. Building upon this, we developed a functional group-based method for predicting new iron-binding molecules. Applying this method to 4,314 natural product molecules from TargetMols Natural Product Library for high throughput screening, we experimentally confirmed that 40 out of the 48 molecules predicted as siderophore candidates possessed iron-binding abilities. Expanding our approach to the COCONUT natural product database, we predicted a staggering 3,199 siderophore candidates, showcasing remarkable structure diversity that are largely unexplored. Our study provides a valuable resource for accelerating the discovery of novel iron-binding molecules and advancing our understanding towards siderophores.

biochemistry↗

bioRxiv2023

The mitochondrial regulation of smooth muscle cell proliferation in type 2 diabetes

BackgroundType 2 diabetes (T2D) is associated with a strongly increased risk for restenosis after angioplasty driven by proliferation of vascular smooth muscle cells (VSMCs). Here, we sought to determine whether and how mitochondrial dysfunction in T2D drives VSMC proliferation with a focus on ROS and intracellular [Ca2+] that both drive cell proliferation, occur in T2D and are regulated by mitochondrial activity. MethodsUsing a diet-induced mouse model of T2D, the inhibition of the mitochondrial Ca2+/calmodulin-dependent kinase II (mtCaMKII), a regulator of Ca2+ entry via the mitochondrial Ca2+ uniporter selectively in VSMCs, we performed in vivo phenotyping after mechanical injury and established the mechanisms of excessive proliferation in cultured VSMCs. ResultsIn T2D, the inhibition of mtCaMKII reduced both neointima formation after mechanical injury and the proliferation of cultured VSMCs. VSMCs from T2D mice displayed accelerated proliferation, reduced mitochondrial Ca2+ entry and membrane potential with elevated baseline [Ca2+]cyto compared to cells from normoglycemic mice. Accelerated proliferation after PDGF treatment was driven by activation of Erk1/2 and its upstream regulators. Hyperactivation of Erk1/2 was Ca2+-dependent rather than mitochondrial ROS-driven Ca2+-dependent and included the activation of CaMKII in the cytosol. The inhibition of mtCaMKII exaggerated the Ca2+ imbalance by lowering mitochondrial Ca2+ entry and increasing baseline [Ca2+]cyto, further enhancing baseline Erk1/2 activation. With inhibition of mtCaMKII, PDGF treatment had no additional effect on cell proliferation. Inhibition of activated CaMKII in the cytosol decreased excessive Erk1/2 activation and reduced VSMC proliferation. ConclusionsCollectively, our results provide evidence for the molecular mechanisms of enhanced VSMC proliferation after mechanical injury by mitochondrial Ca2+ entry in T2D.

molecular biology↗

bioRxiv2023

DPHL v2: An updated and comprehensive DIA pan-human assay library for quantifying more than 14,000 proteins.

A comprehensive pan-human spectral library is critical for biomarker discovery using mass spectrometry (MS)-based proteomics. DPHL v1, a previous pan-human library built from 1096 data-dependent acquisition (DDA) MS data of 16 human tissue types, allows quantifying 10,943 proteins. However, a major limitation of DPHL v1 is the lack of semi-tryptic peptides and protein isoforms, which are abundant in clinical specimens. Here, we generated DPHL v2 from 1608 DDA-MS data acquired using Orbitrap mass spectrometers. The data included 586 DDA-MS newly acquired from 17 tissue types, while 1022 files were derived from DPHL v1. DPHL v2 thus comprises data from 24 sample types, including several cancer types (lung, breast, kidney, and prostate cancer, among others). We generated four variants of DPHL v2 to include semi-tryptic peptides and protein isoforms. DPHL v2 was then applied to a publicly available colorectal cancer dataset with 286 DIA-MS files. The numbers of identified and significantly dysregulated proteins increased by at least 21.7% and 14.2%, respectively, compared with DPHL v1. Our findings show that the increased human proteome coverage of DPHL v2 provides larger pools of potential protein biomarkers.

bioinformatics↗

bioRxiv2023

HERC5-catalyzed ISGylation potentiates cGAS-mediated innate immunity

The key cytosolic DNA sensor cyclic GMP-AMP (cGAMP) synthetase (cGAS) is essential to elicit anti-infection innate immunity whereas aberrant activation of cGAS by endogenous DNA promotes severe autoimmune diseases, thus the activity of cGAS must be strictly regulated to maintain immune homeostasis. Here we report that the E3 ISG15-protein ligase HERC5 interacts with and catalyzes the cGAS ISGylation robustly, whereas the deconjugating enzyme USP18 removes the ISG15 conjugation of cGAS. The interaction of cGAS and HERC5 depends on the cGAS N-terminal domain and the RRC1-4 and HECT domain of HERC5. Mass spectrometry reveals that the Lys21,187,219,458 are the potential ISGylation sites in human cGAS. Deficiency of ISG15 or the E1 ubiquitin-activating enzyme UBA7 greatly attenuate the downstream gene expression induced by cGAS-STING axis and the antiviral ability in mouse and human cells. Collectively, our study uncovered an important role of the HERC5-facilitated cGAS ISGylaion in promoting antiviral defense.

immunology↗

bioRxiv2022

Oncogenic mutations in the DNA-binding domain of FOXO1 disrupt folding: quantitative insights from experiments and molecular simulations

FOXO1, a member of the family of winged-helix motif Forkhead box (FOX) transcription factors, is the most abundantly expressed FOXO member in mature B-cells. Sequencing of diffuse large B-cell lymphoma (DLBCL) tumors and cell lines identified specific mutations in the forkhead domain linked to loss of function. Differential scanning calorimetry and thermal shift assays were used to characterize how eight of these mutations affect the stability of the FOX domain. Mutations L183P and L183R were found to be particularly destabilizing. Electrophoresis mobility shift assays show these same mutations also disrupt FOXO1 binding to their canonical DNA sequences, suggesting the loss of function is due to destabilization of the folded structure. Computational modeling of the effects of mutations on FOXO1 folding was performed using alchemical FEP, and a Markov model of the entire folding reaction was constructed from massively parallel molecular simulations, which predicts folding pathways involving the late folding of helix 3. Although FEP is able to qualitatively predict the destabilization from L183 mutations, we find that a simple hydrophobic transfer model, combined with estimates of unfolded-state solvent accessible surface areas from molecular simulation, is able to more accurately predict changes in folding free energies due to mutations. These results suggest that atomic detail provided from simulation is important for accurate prediction of mutational effects on folding stability. Corresponding disease-associated mutations in other FOX family members support further experimental and computational studies of the folding mechanism of FOX domains.

cancer biology↗

bioRxiv2022

Building an atlas of transposable elements reveals the extensive roles of young SINE in gene regulation, genetic diversity, and complex traits in pigs

Transposable elements (TEs) are an extensive source of genetic polymorphisms and play an indispensable role in chromatin architecture, transcriptional regulatory networks, and genomic evolution. The pig is an important source of animal protein and serves as a biomedical model for humans, yet the functional role of TEs in pigs and their contributions to complex traits are largely unknown. Here, we built a comprehensive catalog of TEs (n = 3,087,929) in pigs by a newly developed pipeline. Through integrating multi-omics data from 21 tissues, we found that SINEs with different ages were significantly associated with genomic regions with distinct functions across tissues. The majority of young SINEs were predominantly silenced by histone modifications, DNA methylation, and decreased accessibility. However, the expression of transcripts that were derived from the remaining active young SINEs exhibited strong tissue specificity through cross-examining 3,570 RNA-seq from 79 tissues and cell types. Furthermore, we detected 211,067 polymorphic SINEs (polySINEs) in 374 individuals genome-wide and found that they clearly recapitulated known patterns of population admixture in pigs. Out of them, 340 population-specific polySINEs were associated with local adaptation. Mapping these polySINEs to genome-wide associations of 97 complex traits in pigs, we found 54 candidate genes (e.g., ANK2 and VRTN) that might be mediated by TEs. Our findings highlight the important roles of young SINEs in functional genomics and provide a supplement for genotype-to-phenotype associations and modern breeding in pigs.

genomics↗

bioRxiv2021

CyanoHABs: inevitable evolutionary ecological consequence for low nutrient-requiring cyanobacteria in water eutrophication

Cyanobacterial harmful algal blooms (CyanoHABs) arise as cyanobacteria dominate phytoplankton communities when nutrient levels increase from oligotrophic state. From a wholistic perspective, this longstanding altered phytoplankton structure results from two conditions: one sufficient condition that cyanobacteria can grow maximally with elevated nutrients; one necessary condition that co-living algae cannot grow fast or dominate at the same levels. The sufficient condition, the special mechanism of CyanoHABs at the population level, has been established as the synergistic interaction between superior cyanobacterial ecophysiology and elevated nutrients. But it is unknown how these functions arise or whether they are under directed evolution to water eutrophication. The necessary condition, the general mechanism of CyanoHABs at the community level, is little understood: why co-living algae cannot form blooms as cyanobacteria? Literature and bioinformatics analyses show that the superior ecophysiology undergoes no directed positive evolution to worldwide eutrophication in general or any local eutrophic waters in particular; instead, these functions are under strong purifying selection and likely acquired through early adaptive radiation in nutrient-deficient conditions, as functions enabling extant cyanobacteria to occupy other niches. The general mechanism turns out to be quite straightforward: cyanobacteria are simple life forms and thus have lower per capita nutrient demand for growth, compared to co-existing eukaryotic algae in cell size and structure, genome size, size of genome-scale metabolic networks, cell content, nutrient requirement. Lower nutrient demand is proved by existing field nutrient supplementation. Both the special and general mechanisms of CyanoHABs are tentative frameworks awaiting further theoretic improvement and empirical assessment.

evolutionary biology↗