Biology subjects

Cao, R.

Publications and source records attributed to Cao, R..

At least 55 records · Page 3Linked to original sources

bioRxiv2023

AnglesRefine: refinement of 3D protein structures using Transformer based on torsion angles

MotivationThe goal of protein structure refinement is to enhance the precision of predicted protein models, particularly at the residue level of the local structure. Existing refinement approaches primarily rely on physics, whereas molecular simulation methods are resource-intensive and time-consuming. In this study, we employ deep learning methods to extract structural constraints from protein structure residues to assist in protein structure refinement. We introduce a novel method, AnglesRefine, which focuses on a proteins secondary structure and employs a transformer model to refine various protein structure angles (psi, phi, omega, CA_C_N_angle, C_N_CA_angle, N_CA_C_angle), ultimately generating a superior protein model based on the refined angles. ResultsWe evaluate our approach against other cutting-edge protein structure refinement methods using the CASP11-14 and CASP15 datasets. Experimental outcomes indicate that our method generally surpasses other techniques on the CASP11-14 test dataset, while performing comparably or marginally better on the CASP15 test dataset. Our method consistently demonstrates the least likelihood of model quality degradation, e.g., the degradation percentage of our method is less than 10%, while other methods are about 50%. Furthermore, as our approach eliminates the need for conformational search and sampling, it significantly reduces computational time compared to existing protein structure refinement methods. Availabilityhttps://github.com/Cao-Labs/AnglesRefine.git Contactcaora@plu.edu CCS CONCEPTS*Computing methodologies [->] Machine learning. ACM Reference FormatLei Zhang, Junyong Zhu, Sheng Wang, Jie Hou, Dong Si, and Renzhi Cao. 2023. AnglesRefine: refinement of 3D protein structures using Transformer based on torsion angles. In Proceedings of 22nd International Workshop on Data Mining in Bioinformatics (BIOKDD 2023) (BIOKDD 2023). ACM, New York, NY, USA, 10 pages. https://doi.org/XXXXXXX.XXXXXXX

bioinformatics↗

bioRxiv2023

Single-shot 3D photoacoustic tomography using a single-element detector for ultrafast imaging of hemodynamics

Imaging hemodynamics is crucial for the diagnosis, treatment, and prevention of vascular diseases. However, current imaging techniques are limited due to the use of ionizing radiation or contrast agents, short penetration depth, or complex and expensive data acquisition systems. Photoacoustic tomography shows promise as a solution to these issues. However, existing photoacoustic tomography methods collect signals either sequentially or through numerous detector elements, leading to either low imaging speed or high system complexity and cost. To address these issues, here we introduce a method to capture a 3D photoacoustic image of vasculature using a single laser pulse and a single-element detector that functions as 6,400 virtual ones. Our method enables ultrafast volumetric imaging of hemodynamics in the human body at up to 1 kHz and requires only a single calibration for different objects and for long-term operations. We demonstrate 3D imaging of hemodynamics at depth in humans and small animals, capturing the variability in blood flow speeds. This concept can inspire other imaging technologies and find applications such as home-care monitoring, biometrics, point-of-care testing, and wearable monitoring.

bioengineering↗

bioRxiv2023

Single neurons in the human medial temporal lobe flexibly shift representations across spatial and memory tasks

Investigations into how individual neurons encode behavioral variables of interest have revealed specific representations in single neurons, such as place and object cells, as well as a wide range of cells with conjunctive encodings or mixed selectivity. However, as most experiments examine neural activity within individual tasks, it is currently unclear if and how neural representations change across different task contexts. Within this discussion, the medial temporal lobe is particularly salient, as it is known to be important for multiple behaviors including spatial navigation and memory, however the relationship between these functions is currently unclear. Here, to investigate how representations in single neurons vary across different task contexts in the MTL, we collected and analyzed single-neuron activity from human participants as they completed a paired-task session consisting of a passive-viewing visual working memory and a spatial navigation and memory task. Five patients contributed 22 paired-task sessions, which were spike sorted together to allow for the same putative single neurons to be compared between the different tasks. Within each task, we replicated concept-related activations in the working memory task, as well as target-location and serial-position responsive cells in the navigation task. When comparing neuronal activity between tasks, we first established that a significant number of neurons maintained the same kind of representation, responding to stimuli presentations across tasks. Further, we found cells that changed the nature of their representation across tasks, including a significant number of cells that were stimulus responsive in the working memory task that responded to serial position in the spatial task. Overall, our results support a flexible encoding of multiple, distinct aspects of different tasks by single neurons in the human MTL, whereby some individual neurons change the nature of their feature coding between task contexts.

neuroscience↗

bioRxiv2022

Open-3DSIM: an Open-source three-dimensional structured illumination microscopy reconstruction platform

With optical section and defocus removal effect, three-dimensional structured illumination microscopy (3DSIM) can get a whole sight of intracellular organelle. Here, Open-3DSIM is reported as an open-source reconstruction platform with double improvement on lateral and axial resolution. MATLAB code, ImageJ version and Exe application are provided for biologists and engineers to maximize its user-friendliness and prompt its further development. Through adaptive parameter estimation and spectrum filter optimization, we demonstrate its superior performance of artifact suppression and defocus elimination over other algorithms on various specimens, under gradient signal-to-noise levels. Moreover, with the capacity to extract the dipole orientation, Open-3DSIM paves a new avenue for interpreting the subcellular structures in six dimensions (xyz{theta}{lambda}t).

bioengineering↗

bioRxiv2022

Japanese Encephalitis Virus NS1 Protein regulates the expression and distribution of TIM-1 to promote viral infection

Japanese encephalitis virus (JEV) is a mosquito-borne Flavivirus, which may cause severe encephalitis in humans, horses, and other animals. TIM-1 has been identified to be a receptor that promotes various viruses to enter into target cells in recent years. In the present study, we found that TIM-1 protein was significantly increased in A549 cells at the late stage of JEV infection, while the transcription levels of TIM-1 remained unaltered. Interestingly, we found that NS1 protein plays a key role in increasing the expression of TIM-1 in cells infected with JEV. Further, we found that the NS1 protein also efficiently regulates TIM-1 protein to distribute in the cytoplasm in JEV-infected cells, and the amount of TIM-1 protein located on the cell membrane was reduced instead. As a consequence, NS1 protein antagonize TIM-1 mediated viral restriction for further viral infection and propagation in the late stage of infection. In molecular mechanism, the molecular weight of TIM-1 increased a bit in the present of NS1. Expression of NEU1 down-regulated TIM-1 expression and oseltamivir treatment increased the expression of TIM-1. Therefore, our data indicated that JEV NS1 protein facilitated the sialylation modification of TIM-1 to up-regulate the level of TIM-1 expression and regulate its distribution. Collectively, our study revealed that JEV NS1 protein regulates the expression and distribution of TIM-1 by facilitating its sialylation to antagonize TIM-1-mediated JEV restriction for further infection. Understanding the functional interplays between TIM-1 and NS1 proteins will offer new insights into virushost interaction. IMPORTANCET-cell immunoglobulin and mucin domain protein 1 (TIM-1) is known to promote cellular entry of various enveloped viruses. We discovered a novel phenomenon of dynamic expression and functional regulation of TIM-1 during JEV infection. Firstly, TIM-1 protein increased in the cytoplasm at the late stage of JEV infection. Furthermore, JEV NS1 protein up-regulated the intracellular expression of TIM-1 and antagonize TIM-1-mediated viral restriction for further viral infection. In molecular mechanism, JEV NS1 protein facilitated the sialylation of TIM-1 to increase the level of TIM-1 expression and cytoplasm distribution. Taken together, at the late stage of infection, JEV employs a strategy in which NS1 promotes JEV release by promoting the sialylation of TIM-1, causing it to be primarily localized in the cytoplasm. Therefore, we discovered new functions of TIM-1 and JEV NS1 during the process of JEV infection, and provide a new insight into the interactions between JEV and cell hosts.

microbiology↗

bioRxiv2022

Temporal and regulatory dynamics of the inner ear transcriptome during development in mice

The inner ear controls hearing and balance, while the temporal molecular signatures and transcriptional regulatory dynamics underlying its development are still unclear. In this study, we investigated time-series transcriptome in the mouse inner ear from embryonic day 11.5 (E11.5) to postnatal day 7 (P7) using bulk RNA-Seq. A total of 10,822 differentially expressed genes were identified between pairwise stages. We identified nine significant temporal expression profiles using time-series expression analysis. The constantly down-regulated profiles throughout the development are related to DNA activity and neurosensory development, while the constantly up-regulated profiles are related to collagen and extracellular matrix. Further co-expression network analysis revealed that several hub genes, such as pnoc1, cd9, and krt27, are related to the neurosensory development, cell adhesion, and keratinization. We uncovered three important transcription regulatory paths during mice inner ear development. Transcription factors related to Hippo/TGF{beta} signaling induced decreased expressions of genes relate to the neurosensory and inner ear development, while a series of INF genes activated the expressions of genes in immunoregulation. In addition to deepening our understanding of the temporal and regulatory mechanisms of inner ear development, our transcriptomic data could fuel future multi-species comparative studies and elucidate the evolutionary trajectory of auditory development.

developmental biology↗

bioRxiv2022

Photoacoustic imaging reveals transient decrease of oxygenation in murine blood due to monoclonal IgG4 antibody

Over 100 monoclonal antibodies have been approved by the FDA for clinical use; however, a paucity of knowledge exists regarding the injection site behavior of these formulated therapeutics, i.e., the effect of antibody and formulation on the tissue around the injection site and vice versa. In this report, we injected a near-infrared dye-labeled IgG4 isotope control antibody into the subcutaneous space in mouse ears to analyze the injection site dynamics, including quantifying molecular movement. Surprisingly, we discovered that the antibody reduces the local blood oxygen saturation levels in mice after prolonged anesthesia without affecting the total hemoglobin content and oxygen extraction fraction. The local oxygen saturation results open a new pathway to study the functional effects of monoclonal antibodies.

immunology↗

bioRxiv2022

Fast and Automated Protein-DNA/RNA Macromolecular Complex Modeling from Cryo-EM Maps

Cryo-electron microscopy (cryo-EM) allows a macromolecular structure such as protein-DNA/RNA complexes to be reconstructed in a three-dimensional coulomb potential map. The structural information of these macromolecular complexes forms the foundation for understanding the molecular mechanism including many human diseases. However, the model building of large macromolecular complexes is often difficult and time-consuming. We recently developed DeepTracer-2.0, an artificial intelligence-based pipeline that can build amino acid and nucleic acid backbones from a single cryo-EM map, and even predict the best-fit residues according to the density of side chains. The experiments showed improved accuracy and efficiency when benchmarking the performance on independent experimental maps of protein-DNA/RNA complexes and demonstrated the promising future of macromolecular modeling from cryo-EM maps. Our method and pipeline could benefit researchers worldwide who work in molecular biomedicine and drug discovery, and substantially increase the throughput of the cryo-EM model building. The pipeline has been integrated into the web portal https://deeptracer.uw.edu/.

bioinformatics↗

bioRxiv2022

An automation workflow for high-throughput manufacturing and analysis of scaffold-supported 3D tissue arrays

The success rate of bringing novel cancer therapies to the clinic remains extremely low due to the lack of relevant pre-clinical culture models that capture the complexity of human tumours. Patient-derived organoids have emerged as a useful tool to model patient and tumour heterogeneity to begin addressing this need. Scaling these complex culture models while enabling stratified analysis of different cellular sub-populations remains a challenge, however. One strategy to enable higher throughput organoid cultures that also enables easy image-based analysis is the Scaffold-supported Platform for Organoid-based Tissues (SPOT) platform. SPOT allows the generation of flat, thin and dimensionally-defined microtissues in both 96- and 384-well plate footprints and is compatible with tumour organoid culture and downstream image-based readouts. SPOT manufacturing is currently a manual process however, limiting the use of SPOT to perform larger-scale screening. In this study, we integrate and optimize an automation approach to generate tumour-mimetic 3D engineered microtissues in SPOT using a liquid handler, and show comparable within-sample and between-sample variation as the standard manual manufacturing process. Furthermore, we develop a liquid handler-supported whole-cell extraction protocol and as a proof-of-value demonstration, we generate 3D complex tissues containing different proportions of tumour and stromal cells and perform single-cell-based end-point analysis to demonstrate the impact of co-culture on the tumour cell population specifically. We also demonstrate we can incorporate primary patient-derived organoids into the pipeline to capture patient-level tumour heterogeneity. We envision that this automated workflow integrated with 96/384-SPOT and multiple cell types and patient-derived organoid models will provide opportunities for future applications in high-throughput screening for novel personalized therapeutic targets. This pipeline also allows the user to assess dynamic cell responses using high-content longitudinal imaging or downstream single-cell-based analyses.

bioengineering↗

bioRxiv2022

An off-the-shelf multi-well scaffold-supported platform for tumour organoid-based tissues

Complex 3D bioengineered tumour models provide the opportunity to better capture the heterogeneity of patient tumours. Patient-derived organoids are emerging as a useful tool to study tumour heterogeneity and variation in patient responses. Organoid cultures typically require a 3D microenvironment that can be manufactured easily to facilitate screening. Here we set out to create a high-throughput, "off-the-shelf" platform which permits the generation of organoid-containing microtissues for standard phenotypic bioassays and image-based readings. To achieve this, we developed the Scaffold-supported Platform for Organoid-based Tissues (SPOT) platform. SPOT is a 3D gel-embedded in vitro platform that can be produced in a 96- or 384-well plate format and enables the generation of flat, thin and dimensionally-defined microgels. SPOT has high potential for adoption due to its reproducible manufacturing methodology, compatibility with existing instrumentation, and reduced within-sample and between-sample variation, which can pose challenges to both data analysis and interpretation. Using SPOT we generate cultures from patient derived pancreatic ductal adenocarcinoma organoids and assess the cellular response to standard-of-care chemotherapeutic compounds, demonstrating our platforms usability for drug screening. We envision 96/384-SPOT will provide a useful tool to assess drug sensitivity of patient-derived organoids and easily integrate into the drug discovery pipeline.

bioengineering↗

bioRxiv2022

Photoacoustic imaging reveals mechanisms of rapid-acting insulin formulations dynamics at the injection site

ObjectiveUltra-rapid insulin formulations control postprandial hyperglycemia; however, inadequate understanding of injection site absorption mechanisms is limiting further advancement. We used photoacoustic imaging to investigate the injection site dynamics of dye-labeled insulin lispro in the Humalog(R) and Lyumjev(R) formulations using the murine ear cutaneous model and correlated it with results from unlabeled insulin lispro in pig subcutaneous injection model. MethodsWe employed dual-wavelength optical-resolution photoacoustic microscopy to study the absorption and diffusion of the near-infrared dye-labeled insulin lispro in the Humalog and Lyumjev formulations in mouse ears. We mathematically modeled the experimental data to calculate the absorption rate constants and diffusion coefficients. We studied the pharmacokinetics of the unlabeled insulin lispro in both the Humalog and Lyumjev formulations as well as a formulation lacking both the zinc and phenolic preservative in pigs. The association state of insulin lispro in each of the formulations was characterized using SV-AUC and NMR spectroscopy. ResultsThrough experiments using murine and swine models, we show that the hexamer dissociation rate of insulin lispro is not the absorption rate-limiting step. We demonstrated that the excipients in the Lyumjev formulation produce local tissue expansion and speed both insulin diffusion and microvascular absorption. We also show that the diffusion of insulin lispro at the injection site drives its initial absorption; however, the rate at which the insulin lispro crosses the blood vessels is its overall absorption rate-limiting step. ConclusionsThis study provides insights into injection site dynamics of insulin lispro and the impact of formulation excipients. It also demonstrates photoacoustic microscopy as a promising tool for studying protein therapeutics. The results from this study address critical questions around the subcutaneous behavior of insulin lispro and the formulation excipients, which could be useful to make faster and better controlled insulin formulations in the future. HighlightsO_LIHexamer dissociation is not the absorption rate-limiting step for insulin lispro C_LIO_LILyumjev excipients enhance insulin microvascular absorption and diffusion C_LIO_LIVascular endothelial transit determines the overall absorption for insulin lispr C_LIO_LIInsulin diffusion studied for the first time at the injection site of live animals C_LIO_LIIn vivo imaging is a powerful tool to study injection site dynamics C_LI

systems biology↗

bioRxiv2022

Rational evolution of a recombinant DNA polymerase for efficient incorporation of unnatural nucleotides by dual-site boosting

Machine learning modelling assisting function-oriented enzyme engineering is normally built on predefined protein sequence space. However, efficient defining the determinant amino acid positions upon which the combinatorial mutation library is constructed is still a challenge in protein science. Herein, we present a comprehensive investigation of modifying a recombinant DNA polymerase for efficient incorporating one unnatural nucleotide, including the identification of key sites/regions, machine learning-assisted mutants screening, and the underlying mechanism of kinetics boosting. By using hundreds of training points and only dozens of testing samples, we found that one highly engineered enzymes catalytic efficiency can be further improved by one order of magnitude by specific mutation on two sites, 485I and 451L. Compared to the position 485 which is known to dominate local conformation of B-family DNA polymerases, 451 is a split-new active site discovered by our approach. A novel allosteric regulation mechanism is underlying the apparent synergy of 485I and 451L on the kinetics boosting. As a result, a "half-closed" conformation of the binding pocket and a cooperative binding of both primer and template DNA strands on the protein accelerated the processes of substrates incorporation, molecular recognition, and releasing of incorrect nucleotides. These findings have implications in guiding the function-tuning of DNA polymerases for a broad range of biotechnological applications.

biochemistry↗

bioRxiv2021

Hypothermia Suppresses Uncoupling of Oxidative-Phosphorylation after Neonatal Cerebral Hypoxia-Ischemia

Hypoxia-ischemia (HI), which disrupts the oxygen supply-demand balance in the brain by impairing blood oxygen supply and the cerebral metabolic rate of oxygen (CMRO2), is a leading cause of neonatal brain injury. However, it is unclear how post-HI hypothermia helps to restore the balance, as cooling reduces CMRO2. Also, how transient HI leads to secondary energy failure (SEF) in neonatal brains remains elusive. Using photoacoustic microscopy, we examined the effects of HI on CMRO2 in awake 10-day-old mice, supplemented by bioenergetic analysis of purified cortical mitochondria. Our results show that while HI suppresses ipsilateral CMRO2, it sparks a prolonged CMRO2-surge post-HI, associated with increased mitochondrial oxygen consumption, superoxide emission, and reduced mitochondrial membrane potential necessary for ATP synthesis--indicating oxidative phosphorylation (OXPHOS) uncoupling. Post-HI hypothermia prevents the CMRO2-surge by constraining oxygen extraction fraction, reduces mitochondrial oxidative stress, and maintains ATP and N-acetylaspartate levels, resulting in attenuated infarction at 24 hours post-HI. Our findings suggest that OXPHOS-uncoupling induced by the post-HI CMRO2-surge underlies SEF and blocking the surge is a key mechanism of hypothermia protection. Also, our study highlights the potential of optical CMRO2-measurements for detecting neonatal HI brain injury and guiding the titration of therapeutic hypothermia at the bedside.

neuroscience↗

bioRxiv2021

Distinct neurocognitive bases for social trait judgments of faces in autism spectrum disorder

Autism spectrum disorder (ASD) is characterized by difficulties in social processes, interactions, and communication. Yet, the neurocognitive bases underlying these difficulties are unclear. Here, we triangulated the trans-diagnostic approach to personality, social trait judgments of faces, and neurophysiology to investigate (1) the relative position of autistic traits in a comprehensive social-affective personality space and (2) the distinct associations between the social-affective personality dimensions and social trait judgment from faces in individuals with ASD and neurotypical individuals. We collected personality and facial judgment data from a large sample of online participants (N = 89 self-identified ASD; N = 308 neurotypical controls). Factor analysis with 33 sub-scales of 10 social-affective personality questionnaires identified a 4-dimensional personality space. This analysis revealed that ASD and control participants did not differ significantly along the personality dimensions of empathy and prosociality, antisociality, or social agreeableness. However, the associations between these dimensions and judgments of facial trustworthiness and warmth differed across groups. Neurophysiological data also indicated that ASD and control participants might rely on distinct neuronal representations for judging trustworthiness and warmth from faces. These results suggest that the atypical association between social-affective personality and social trait judgment from faces may contribute to the social and affective difficulties associated with ASD.

neuroscience↗

bioRxiv2021

Emergence of an adaptive epigenetic cell state in human bladder urothelial carcinoma evolution

Intratumor heterogeneity (ITH) of bladder cancer (BLCA) facilitates therapy resistance and immune evasion to affect clinical prognosis directly. However, the molecular and cellular mechanism generating ITH in BLCA remains elusive. Here we show that a TM4SF1-positive cancer subpopulation (TPCS) drives ITH diversification in BLCA. By extensive profiling of the epigenome and transcriptome of BLCA from 79 donors across all stages, we elucidated the evolution trajectories of luminal and basal BLCA. TPCS emerges from the basal trajectory and shows extensive transcriptional plasticity with a distinct epigenomic landscape. Clinically, TPCS were enriched in advanced stage patients and associated with poor prognosis. Our results showed how cancer adapts to its environment by adopting a stem cell-like epigenomic landscape.

cancer biology↗

bioRxiv2021

Internally Generated Time in the Rodent Hippocampus is Logarithmically Compressed

The Weber-Fechner law proposes that our perceived sensory input increases with physical input on a logarithmic scale. Hippocampal "time cells" carry a record of recent experience by firing sequentially during a circumscribed period of time after a triggering stimulus. Different cells have "time fields" at different delays up to at least tens of seconds. Past studies suggest that time cells represent a compressed timeline by demonstrating that fewer time cells fire late in the delay and their time fields are wider. This paper asks whether the compression of time cells obeys the Weber-Fechner Law. Time cells were studied with a hierarchical Bayesian model that simultaneously accounts for the firing pattern at the trial level, cell level, and population level. This procedure allows separate estimates of the within-trial receptive field width and the across-trial variability. After isolating across-trial variability, time field width increased linearly with delay. Further, the time cell population was distributed evenly along a logarithmic time axis. These findings provide strong quantitative evidence that the neural temporal representation in rodent hippocampus is logarithmically compressed and obeys a neural Weber-Fechner Law.

neuroscience↗

bioRxiv2021

SOD1 Mediates Lysosome-to-Mitochondria Communication and its Dysregulation by Amyloid-β Oligomers

Altered mitochondrial DNA (mtDNA) occurs in neurodegenerative disorders like Alzheimers disease (AD); how mtDNA synthesis is linked to neurodegeneration is poorly understood. We discovered Nutrient-induced Mitochondrial Activity (NiMA), an inter-organelle signaling pathway where nutrient-stimulated lysosomal mTORC1 activity regulates mtDNA replication in neurons by a mechanism sensitive to amyloid-{beta} oligomers (A{beta}Os), a primary factor in AD pathogenesis. Using 5-ethynyl-2-deoxyuridine (EdU) incorporation into mtDNA of cultured neurons, along with photoacoustic and mitochondrial metabolic imaging of cultured neurons and mouse brains, we show these effects being mediated by mTORC1-catalyzed T40 phosphorylation of superoxide dismutase 1 (SOD1). Mechanistically, tau, another key factor in AD pathogenesis and other tauopathies, reduced the lysosomal content of the tuberous sclerosis complex (TSC), thereby increasing NiMA and suppressing SOD1 activity and mtDNA synthesis. A{beta}Os inhibited these actions. Dysregulation of mtDNA synthesis was observed in fibroblasts derived from TS patients, who lack functional TSC and elevated SOD1 activity was also observed in human AD brain. Together, these findings imply that tau and SOD1 couple nutrient availability to mtDNA replication, linking mitochondrial dysfunction to AD.

neuroscience↗

bioRxiv2021

Targeted degradation of the oncogenic phosphatase SHP2

SHP2 is a protein tyrosine phosphatase that plays a critical role in the full activation of the Ras/MAPK pathway upon stimulation of receptor tyrosine kinases (RTKs), which are frequently amplified or mutationally activated in human cancer. In addition, activating mutations in SHP2 result in developmental disorders and hematologic malignancies. Several allosteric inhibitors have been developed for SHP2 and are currently in clinical trials. Here, we report the development and evaluation of a SHP2 PROTAC created by conjugating RMC-4550 with pomalidomide using a PEG linker. This molecule is highly selective for SHP2, induces degradation of SHP2 in leukemic cells at sub-micromolar concentration, inhibits MAPK signaling, and suppresses cancer cell growth. SHP2 PROTACs serve as an alternative strategy for targeting ERK-dependent cancers and are useful tools alongside allosteric inhibitors for dissecting the mechanisms by which SHP2 exerts its oncogenic activity.

biochemistry↗