Shuo Huang

Nanjing University

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Panke Zhang

Nanjing University

Yuqin Wang

Shaanxi Normal University

Shanyu Zhang

Anhui Medical University

Hong‐Yuan Chen

Nanjing University

Shuanghong Yan

Affiliated Hospital of Hangzhou Normal University

Wendong Jia

Nanjing University

Xiaoyu Du

Nanjing University

Pingping Fan

Anhui Agricultural University

Liying Wang

National Institute for Parasitic Diseases

Yao Liu

Huazhong University of Science and Technology

Cooperative Institutions

Peking University

Chinese Academy of Sciences

Nanjing University

Peking University Third Hospital

Sun Yat-sen University

Chinese Academy of Medical Sciences & Peking Union Medical College

Shanghai Jiao Tong University

Ministry of Education of the People's Republic of China

University of Chinese Academy of Sciences

Central South University

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Discrimination of Ribonucleoside Mono-, Di-, and Triphosphates Using an Engineered Nanopore

ACS Nano (2022)

Yuqin Wang Pingping Fan Shanyu Zhang Liying Wang Xinyue Li

Ribonucleotides, which widely exist in all living organisms and are essential to both physiological and pathological processes, can naturally appear as ribonucleoside mono-, di-, and triphosphates. Natural ribonucleotides can also dynamically switch between different phosphorylated forms, posing a great challenge for sensing. A specially engineered nanopore sensor is promising for full discrimination of all canonical ribonucleoside mono-, di-, and triphosphates. However, such a demonstration has never been reported, due to the lack of a suitable nanopore sensor that has a sufficient resolution. In this work, we utilized a phenylboronic acid (PBA) modified Mycobacterium smegmatis porin A (MspA) hetero-octamer for ribonucleotide sensing. Twelve types of ribonucleotides, including mono-, di-, and triphosphates of cytidine (CMP, CDP, CTP), uridine (UMP, UDP, UTP), adenosine (AMP, ADP, ATP), and guanosine (GMP, GDP, GTP) were simultaneously discriminated. A machine-learning algorithm was also developed, which achieved a general accuracy of 99.9% for ribonucleotide sensing. This strategy was also further applied to identify ribonucleotide components in ATP tablets and injections. This sensing strategy provides a direct, accurate, easy, and rapid solution to characterize ribonucleotide components in different phosphorylated forms.

Ribonucleotide

Ribonucleoside

Cytidine

Nanopore

Inosine

10.1021/acsnano.2c09662

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Citations (18)

Numerical calculation and model experiment of a novel external buoy type wave energy converter for navigation lighted buoys numerical study of a novel wave energy converter

IET Renewable Power Generation (2021)

Shuo Huang Weiqi Liu Chao Zhang Songwei Sheng Yage You

Abstract A novel external buoy type wave energy device with hydraulic conversion system used for navigation lighted buoys, named floating external double buoys wave energy device, is put forward and investigated by numerical calculations and model experiments. The hydrodynamic performance of the device under regular waves is numerically calculated based on linear potential flow theory and boundary element method. The generalized modal method is used to solve the hydrodynamic problems of multi‐buoy with hinged constraints. The model experiments are carried out in a 2D wave tank with a depth of 0.9 m. The wave height is set to 1/40 of the wavelength. The influence of wave period and damping loads on the hydrodynamic performance of the device is tested. The results of numerical calculations and model experiments have shown that the appropriate selection of hydraulic damping coefficient is of great significance to improve the capture width ratio of the device, and this device has good capture performance in a certain wave range, and it is expected to effectively solve the problem of continuous power supply for middle and small types of navigation lighted buoys.

Buoy

Energy transformation

10.1049/rpg2.12279

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Citations (2)

A particle-in-cell/Monte Carlo simulation of a capacitively coupled chlorine discharge

Bulletin of the American Physical Society (2013)

Jón Tómas Guðmundsson Shuo Huang

Particle-in-cell

Source

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Citations (0)

Corrigendum: A Novel Antioxidant Protects Against Contrast Medium-Induced Acute Kidney Injury in Rats

Frontiers in Pharmacology (2021)

Shuo Huang Yanyan Tang Tianjun Liu Ning Zhang Xueyan Yang

CORRECTION article Front. Pharmacol., 09 July 2021Sec. Experimental Pharmacology and Drug Discovery https://doi.org/10.3389/fphar.2021.724416

10.3389/fphar.2021.724416

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A Nanopore‐Based Saccharide Sensor

Angewandte Chemie International Edition (2022)

Shanyu Zhang Zhenyuan Cao Pingping Fan Yuqin Wang Wendong Jia

Abstract Saccharides play critical roles in many forms of cellular activities. Saccharide structures are however complicated and similar, setting a technical hurdle for direct identification. Nanopores, which are emerging single molecule tools sensitive to minor structural differences between analytes, can be engineered to identity saccharides. A hetero‐octameric Mycobacterium smegmatis porin A nanopore containing a phenylboronic acid was prepared, and was able to clearly identify nine monosaccharide types, including D‐fructose, D‐galactose, D‐mannose, D‐glucose, L‐sorbose, D‐ribose, D‐xylose, L‐rhamnose and N‐acetyl‐D‐galactosamine. Minor structural differences between saccharide epimers can also be distinguished. To assist automatic event classification, a machine learning algorithm was developed, with which a general accuracy score of 0.96 was achieved. This sensing strategy is generally suitable for other saccharide types and may bring new insights to nanopore saccharide sequencing.

Nanopore

Monosaccharide

Rhamnose

10.1002/anie.202203769

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Citations (59)

Insulated gold scanning tunneling microscopy probes for recognition tunneling in an aqueous environment

Review of Scientific Instruments (2012)

Michael R. Tuchband Jin He Shuo Huang Stuart Lindsay

Chemically functionalized probes are required for tunneling measurements made via chemical contacts (“Recognition Tunneling”). Here, we describe the etching of gold STM probes suitable for chemical functionalization with moieties bearing thiol groups. Insulated with high density polyethylene, these probes may be used in aqueous electrolytes with sub pA leakage currents. The area of the exposed probe surface was characterized via the saturation current in an electroactive solution (0.1 M K3Fe(CN)6). Twenty five percent of the probes had an exposed region of 10 nm radius or less.

Surface Modification

Isotropic etching

Saturation (graph theory)

Scanning Probe Microscopy

10.1063/1.3673640

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Citations (35)

Shape optimization design of a heaving buoy of wave energy converter based on fully parametric modeling and CFD method

Journal of Hydrodynamics (2022)

Shuo Huang Weiqi Liu Kai Wang Tiecheng Wu Tianhui Liu

Buoy

10.1007/s42241-022-0080-x

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Citations (3)

Transcriptome analysis of PCOS arrested 2-cell embryos

Cell Cycle (2018)

Cuiling Lu Hongbin Chi Yapeng Wang Xue Feng Lina Wang

In an attempt to explore the early developmental arrest in embryos from polycystic ovarian syndrome (PCOS) patients, we sequenced the transcriptome profiles of PCOS arrested 2-cell embryos, non-PCOS arrested 2-cell embryos and non-arrested 2-cell embryos using single-cell RNA-Seq technique. Differential expression analysis was performed using the DEGSeq R package. Gene Ontology (GO) enrichment was analyzed using the GOseq R package. Data revealed 62 differentially expressed genes between non-PCOS arrested and PCOS arrested embryos and 2217 differentially expressed genes between PCOS arrested and non-arrested 2-cell embryos. A total of 49 differently expressed genes (DEGs) were annotated with GO terms in the up-regulated genes between PCOS arrested and non-PCOS arrested embryos after GO enrichment. A total of 29 DEGs were annotated with GO terms in the down-regulated genes between PCOS arrested and non-arrested 2-cell embryos after GO enrichment. These data can provide a reference for screening specific genes involved in the arrest of PCOS embryos.

10.1080/15384101.2018.1467678

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Citations (9)

Identifying single bases in a DNA oligomer with electron tunnelling

Nature Nanotechnology (2010)

Shuo Huang Jin He Shuai Chang Peiming Zhang Feng Liang

Oligomer

Nanopore

Nucleobase

10.1038/nnano.2010.213

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Citations (283)

Machine Learning Assisted Simultaneous Structural Profiling of Differently Charged Proteins in a Mycobacterium smegmatis Porin A (MspA) Electroosmotic Trap

Journal of the American Chemical Society (2022)

Yao Liu Kefan Wang Yuqin Wang Liying Wang Shuanghong Yan

The nanopore is emerging as a means of single-molecule protein sensing. However, proteins demonstrate different charge properties, which complicates the design of a sensor that can achieve simultaneous sensing of differently charged proteins. In this work, we introduce an asymmetric electrolyte buffer combined with the Mycobacterium smegmatis porin A (MspA) nanopore to form an electroosmotic flow (EOF) trap. Apo- and holo-myoglobin, which differ in only a single heme, can be fully distinguished by this method. Direct discrimination of lysozyme, apo/holo-myoglobin, and the ACTR/NCBD protein complex, which are basic, neutral, and acidic proteins, respectively, was simultaneously achieved by the MspA EOF trap. To automate event classification, multiple event features were extracted to build a machine learning model, with which a 99.9% accuracy is achieved. The demonstrated method was also applied to identify single molecules of α-lactalbumin and β-lactoglobulin directly from whey protein powder. This protein-sensing strategy is useful in direct recognition of a protein from a mixture, suggesting its prospective use in rapid and sensitive detection of biomarkers or real-time protein structural analysis.

Mycobacterium smegmatis

Porin

Nanopore

10.1021/jacs.1c09259

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Citations (46)