Songtao Ye

ORCID: 0009-0004-1959-4918
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About
Contact & Profiles
Research Areas
  • Innovative Microfluidic and Catalytic Techniques Innovation
  • RNA Research and Splicing
  • Luminescence and Fluorescent Materials
  • Protein purification and stability
  • Advanced Fluorescence Microscopy Techniques
  • Molecular Sensors and Ion Detection
  • Protein Structure and Dynamics
  • Polyoxometalates: Synthesis and Applications
  • Proteins in Food Systems
  • Cellular Mechanics and Interactions
  • Connective tissue disorders research
  • RNA modifications and cancer
  • Photoreceptor and optogenetics research
  • Metal-Organic Frameworks: Synthesis and Applications
  • Covalent Organic Framework Applications
  • Pluripotent Stem Cells Research
  • Biotin and Related Studies
  • Analytical Chemistry and Chromatography
  • Mesoporous Materials and Catalysis
  • Single-cell and spatial transcriptomics
  • Nuclear Structure and Function
  • Supramolecular Chemistry and Complexes
  • Pancreatic function and diabetes
  • Zebrafish Biomedical Research Applications
  • Click Chemistry and Applications

Westlake University
2022-2025

Massachusetts Institute of Technology
2024

Zhejiang University
2024

University of Cambridge
2024

Xi'an Jiaotong University
2024

University of California, Merced
2021-2023

Institute of Natural Science
2023

Pennsylvania State University
2020-2022

University of Akron
2018-2020

Molecular rotor-based fluorophores (RBFs) have been widely used in many fields. However, the lack of control their viscosity sensitivity limits application. Herein, this problem is resolved by chemically installing extended π-rich alternating carbon-carbon linkages between rotational electron donors and acceptors RBFs. The data reveal that length linkage strongly influences sensitivity, likely resulting from varying height energy barriers fluorescent planar dark twisted configurations. Three...

10.1002/anie.202011108 article EN Angewandte Chemie International Edition 2020-09-29

Aberrantly processed or mutant proteins misfold and assemble into a variety of soluble oligomers insoluble aggregates, process that is associated with an increasing number diseases are not curable manageable. Herein, we present chemical toolbox, AggFluor, allows for live cell imaging differentiation complex aggregated conformations in cells. Based on the chromophore core green fluorescent proteins, AggFluor comprised series molecular rotor fluorophores span wide range viscosity sensitivity....

10.1021/jacs.0c07245 article EN Journal of the American Chemical Society 2020-09-11

Protein aggregation is a biological phenomenon in which aberrantly processed or mutant proteins misfold and assemble into variety of insoluble aggregates. Decades studies have delineated the structure, interaction, activity either their natively folded structures aggregates such as amyloid fibrils. However, intermediate species exist between these two extreme states protein folding landscape. Herein, we collectively term misfolded oligomers, including soluble oligomers preamyloid that are...

10.1021/acs.accounts.1c00648 article EN Accounts of Chemical Research 2022-01-18

Abstract Fluorescence lifetime imaging has been a powerful tool for biomedical research. Recently, fluorescence lifetime‐based multiplexing expanded channels by using probes that harbor the same spectral and distinct excited state lifetime. While it is desirable to control of any given fluorescent probes, rational lifetimes remains challenge. Herein, we chose boron dipyrromethene (BODIPY) as model system provided chemical strategies regulate its derivatives with varying features. We find...

10.1002/anie.202403029 article EN Angewandte Chemie International Edition 2024-04-20

Abstract Aberrant protein aggregation leads to various human diseases, but little is known about the physical chemical properties of these aggregated proteins in cells. Herein, we developed a boron‐dipyrromethene (BODIPY)‐based HaloTag probe, whose conjugation HaloTag‐fused allows us study aggregates using both fluorescence intensity and lifetime. Modulation BODIPY fluorophore reveals key structural features attain dual function. The optimized probe exhibits increased elongated lifetime...

10.1002/agt2.301 article EN cc-by Aggregate 2022-12-19

A series of rod-shaped polyoxometalates (POMs) [Bu4 N]7 [Mo6 O18 NC(CH2 O)3 MnMo6 (OCH2 )3 CNMo6 ] and [ArNMo6 O17 NAr] (Ar=2,6-dimethylphenyl, naphthyl 1-methylnaphthyl) were chosen to study the effects cation-π interaction on macroionic self-assembly. Diffusion ordered spectroscopy (DOSY) isothermal titration calorimetry (ITC) techniques show that binding affinity between POMs Zn2+ ions is enhanced significantly after grafting aromatic groups onto clusters, leading effective replacement...

10.1002/anie.201800409 article EN Angewandte Chemie International Edition 2018-02-14

The formation of cellular condensates, akin to membraneless organelles, is typically mediated by liquid-liquid phase separation (LLPS), during which proteins and RNA molecules interact with each other via multivalent interactions. Gaining a comprehensive understanding these interactions holds significance in unraveling the mechanisms underlying condensate pathology related diseases. In an attempt toward this end, fluorescence microscopy often used examine colocalization target proteins/RNAs....

10.1091/mbc.e23-11-0442 article EN Molecular Biology of the Cell 2024-01-17

The phase separation of intrinsically disordered proteins is emerging as an important mechanism for cellular organization. However, efforts to connect protein sequences the physical properties condensates, that is, molecular grammar, are hampered by a lack effective approaches probing high-resolution structural details. Using combination multiscale simulations and fluorescence lifetime imaging microscopy experiments, we systematically explored series systems consisting diblock elastin-like...

10.7554/elife.90750.4 article EN cc-by eLife 2025-03-26

10.1016/j.tibs.2025.03.008 article EN Trends in Biochemical Sciences 2025-04-01

Human pluripotent stem cell (hPSC)-derived pancreatic progenitors (PPs) provide promising therapies for type 1 diabetes. Current PP differentiation requires a high amount of Activin A during the definitive endoderm (DE) stage, making it economically difficult commercial ventures. Here we identify dose-dependent role Wnt signaling in controlling DE without A. While high-level activation induces mesodermal formation, low-level by small-molecule inhibitor glycogen synthase kinase 3 is...

10.1016/j.stemcr.2021.07.021 article EN cc-by Stem Cell Reports 2021-08-26

Abstract Microenvironment is critical to the function of cells and organisms. One example provided by biomolecular condensates, whose microenvironment can be vastly different from surrounding cellular environments engage unique biological functions. How microenvironments condensates affect their structure remains unknown. Here, we show that arrangements partitioning biomolecules are dictated differences between micropolarity each subcompartment. Sufficient difference in results layered...

10.1101/2023.03.30.534881 preprint EN cc-by-nc-nd bioRxiv (Cold Spring Harbor Laboratory) 2023-03-30

Automatic road extraction from satellite images is a popular research hotspot topic in the field of remote sensing. However, complexity features and structures hinders their precise extraction. Road have different saliency due to occlusion other objects diverse types. are scattered across various locations affected by geographical conditions, population distribution, transportation demands. These issues render current methods based on convolutional neural networks prone fragmented incomplete...

10.1016/j.jksuci.2024.102009 article EN cc-by-nc-nd Journal of King Saud University - Computer and Information Sciences 2024-03-01

There is an unmet demand for research tools to monitor the multistep protein aggregation process in live cells, a that has been associated with growing number of human diseases. Recently, AIEgens have developed directly entire test tubes and cells. Future application expected shed light on both diagnosis treatment disease rooted aggregation.

10.1093/nsr/nwab013 article EN cc-by National Science Review 2021-01-23

We report a distinctive trend in the binding affinity of metal cations when they interact with lacunary Keggin-type polyoxometalate K7[α-PW11O39] clusters aqueous media. The follows special trends Li+ > Na+ K+ for monovalent and Mg2+ Ca2+ Sr2+ Ba2+ divalent cations, completely reversed from common < macroion–counterion ion-pair formation dilution solution. Isothermal titration calorimetry NMR measurements confirm that hydration shells are significantly broken during interaction nanoscale...

10.1021/acs.jpcc.9b03004 article EN The Journal of Physical Chemistry C 2019-05-22

The phase separation of intrinsically disordered proteins is emerging as an important mechanism for cellular organization. However, efforts to connect protein sequences the physical properties condensates, i.e., molecular grammar, are hampered by a lack effective approaches probing high-resolution structural details. Using combination multiscale simulations and fluorescence lifetime imaging microscopy experiments, we systematically explored series systems consisting diblock elastin-like...

10.1101/2023.03.30.534967 preprint EN cc-by-nc-nd bioRxiv (Cold Spring Harbor Laboratory) 2023-04-02

The phase separation of intrinsically disordered proteins is emerging as an important mechanism for cellular organization. However, efforts to connect protein sequences the physical properties condensates, i.e., molecular grammar, are hampered by a lack effective approaches probing high-resolution structural details. Using combination multiscale simulations and fluorescence lifetime imaging microscopy experiments, we systematically explored series systems consisting diblock elastin-like...

10.7554/elife.90750.3 preprint EN 2024-05-07

Abstract Molecular rotor‐based fluorophores (RBFs) have been widely used in many fields. However, the lack of control their viscosity sensitivity limits application. Herein, this problem is resolved by chemically installing extended π‐rich alternating carbon‐carbon linkages between rotational electron donors and acceptors RBFs. The data reveal that length linkage strongly influences sensitivity, likely resulting from varying height energy barriers fluorescent planar dark twisted...

10.1002/ange.202011108 article EN Angewandte Chemie 2020-09-29

Abstract A series of rod‐shaped polyoxometalates (POMs) [Bu 4 N] 7 [Mo 6 O 18 NC(CH 2 O) 3 MnMo (OCH ) CNMo ] and [ArNMo 17 NAr] (Ar=2,6‐dimethylphenyl, naphthyl 1‐methylnaphthyl) were chosen to study the effects cation–π interaction on macroionic self‐assembly. Diffusion ordered spectroscopy (DOSY) isothermal titration calorimetry (ITC) techniques show that binding affinity between POMs Zn 2+ ions is enhanced significantly after grafting aromatic groups onto clusters, leading effective...

10.1002/ange.201800409 article EN Angewandte Chemie 2018-02-14

Lactic acid-functionalized chiral fullerene (C60) molecules are used as models to understand selection in macroionic solutions involving macroions, counterions, and/or co-ions. With the addition of Zn2+ cations, C60 macroions exhibit slow self-assembly behavior into hollow, spherical, blackberry-type structures, confirmed by laser light scattering (LLS), transmission electron microscopy (TEM), and atomic force (AFM) techniques. Chiral counterions with high charge density show no chirality...

10.1021/acs.langmuir.0c00611 article EN Langmuir 2020-04-15

Measuring the diffusivity of molecules is first step toward understanding their dependence and controlling diffusion, but challenge increases with decrease molecular size, particularly for non-fluorescent non-reactive such as solvents. Here, capability to monitor solvent exchange process within micropores silica millisecond time resolution demonstrated, by simply embedding a rotor-based fluorophore (thioflavin T) in colloidal nanoparticles. Basically, provides an extreme case viscous...

10.1002/adma.202305779 article EN Advanced Materials 2023-09-29

The phase separation of intrinsically disordered proteins is emerging as an important mechanism for cellular organization. However, efforts to connect protein sequences the physical properties condensates, i.e., molecular grammar, are hampered by a lack effective approaches probing high-resolution structural details. Using combination multiscale simulations and fluorescence lifetime imaging microscopy experiments, we systematically explored series systems consisting diblock elastin-like...

10.7554/elife.90750.1 preprint EN 2023-11-21

The phase separation of intrinsically disordered proteins is emerging as an important mechanism for cellular organization. However, efforts to connect protein sequences the physical properties condensates, that is, molecular grammar, are hampered by a lack effective approaches probing high-resolution structural details. Using combination multiscale simulations and fluorescence lifetime imaging microscopy experiments, we systematically explored series systems consisting diblock elastin-like...

10.7554/elife.90750 article EN cc-by eLife 2023-11-21

Fluorescent proteins (FPs) have gained much attention over the last few decades as powerful tools in bioimaging since discovery of green fluorescent protein (GFP) 1960s. The mechanism FP bioluminenscence has been well-studied, and new variants with improved photophysical properties are being constantly generated. In this review, a brief history GFP along its biogenesis is first provided. Next, quenching governing property elaborated. Most importantly, we seek to introduce expanding family...

10.1063/5.0080417 article EN Chemical Physics Reviews 2022-02-22
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