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Article ; Online: Systematic analysis of the impact of phosphorylation and O-GlcNAcylation on protein subcellular localization

Senhan Xu / Suttipong Suttapitugsakul / Ming Tong / Ronghu Wu

Cell Reports, Vol 42, Iss 7, Pp 112796- (2023)

2023

Abstract: Summary: The subcellular localization of proteins is critical for their functions in eukaryotic cells and is tightly correlated with protein modifications. Here, we comprehensively investigate the nuclear-cytoplasmic distributions of the phosphorylated, ... ...

Abstract	Summary: The subcellular localization of proteins is critical for their functions in eukaryotic cells and is tightly correlated with protein modifications. Here, we comprehensively investigate the nuclear-cytoplasmic distributions of the phosphorylated, O-GlcNAcylated, and non-modified forms of proteins to dissect the correlation between protein distribution and modifications. Phosphorylated and O-GlcNAcylated proteins have overall higher nuclear distributions than non-modified ones. Different distributions among the phosphorylated, O-GlcNAcylated, and non-modified forms of proteins are associated with protein size, structure, and function, as well as local environment and adjacent residues around modification sites. Moreover, we perform site-mutagenesis experiments using phosphomimetic and phospho-null mutants of two proteins to validate the proteomic results. Additionally, the effects of the OGT/OGA inhibition on glycoprotein distribution are systematically investigated, and the distribution changes of glycoproteins are related to their abundance changes under the inhibitions. Systematic investigation of the relationship between protein modification and localization advances our understanding of protein functions.
Keywords	CP: Molecular biology ; Biology (General) ; QH301-705.5
Subject code	612
Language	English
Publishing date	2023-07-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Concordant and Discordant Cerebrospinal Fluid and Plasma Cytokine and Chemokine Responses in Mild Cognitive Impairment and Early-Stage Alzheimer’s Disease

Suzanne M. de la Monte / Ming Tong / Andrew J. Hapel

Biomedicines, Vol 11, Iss 2394, p

2023 Volume 2394

Abstract: Neuroinflammation may be a pathogenic mediator and biomarker of neurodegeneration at the boundary between mild cognitive impairment (MCI) and early-stage Alzheimer’s disease (AD). Whether neuroinflammatory processes are endogenous to the central nervous ... ...

Abstract	Neuroinflammation may be a pathogenic mediator and biomarker of neurodegeneration at the boundary between mild cognitive impairment (MCI) and early-stage Alzheimer’s disease (AD). Whether neuroinflammatory processes are endogenous to the central nervous system (CNS) or originate from systemic (peripheral blood) sources could impact strategies for therapeutic intervention. To address this issue, we measured cytokine and chemokine immunoreactivities in simultaneously obtained lumbar puncture cerebrospinal fluid (CSF) and serum samples from 39 patients including 18 with MCI or early AD and 21 normal controls using a 27-plex XMAP bead-based enzyme-linked immunosorbent assay (ELISA). The MCI/AD combined group had significant ( p < 0.05 or better) or statistically trend-wise (0.05 ≤ p ≤ 0.10) concordant increases in CSF and serum IL-4, IL-5, IL-9, IL-13, and TNF-α and reductions in GM-CSF, b-FGF, IL-6, IP-10, and MCP-1; CSF-only increases in IFN-y and IL-7 and reductions in VEGF and IL-12p70; serum-only increases in IL-1β, MIP-1α, and eotaxin and reductions in G-CSF, IL-2, IL-8 and IL-15; and discordant CSF–serum responses with reduced CSF and increased serum PDGF-bb, IL-17a, and RANTES. The results demonstrate simultaneously parallel mixed but modestly greater pro-inflammatory compared to anti-inflammatory or neuroprotective responses in CSF and serum. In addition, the findings show evidence that several cytokines and chemokines are selectively altered in MCI/AD CSF, likely corresponding to distinct neuroinflammatory responses unrelated to systemic pathologies. The aggregate results suggest that early management of MCI/AD neuroinflammation should include both anti-inflammatory and pro-neuroprotective strategies to help prevent disease progression.
Keywords	Alzheimer’s ; lumbar spinal fluid ; plasma ; cytokines ; cognitive dysfunction ; inflammation ; Biology (General) ; QH301-705.5
Subject code	616
Language	English
Publishing date	2023-08-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Spatial and temporal proteomics reveals the distinct distributions and dynamics of O-GlcNAcylated proteins

Senhan Xu / Ming Tong / Suttipong Suttapitugsakul / Ronghu Wu

Cell Reports, Vol 39, Iss 11, Pp 110946- (2022)

2022

Abstract: Summary: Protein O-GlcNAcylation plays critical roles in many cellular events, and its dysregulation is related to multiple diseases. Integrating bioorthogonal chemistry and multiplexed proteomics, we systematically and site specifically study the ... ...

Abstract	Summary: Protein O-GlcNAcylation plays critical roles in many cellular events, and its dysregulation is related to multiple diseases. Integrating bioorthogonal chemistry and multiplexed proteomics, we systematically and site specifically study the distributions and dynamics of protein O-GlcNAcylation in the nucleus and the cytoplasm of human cells. The results demonstrate that O-GlcNAcylated proteins with different functions have distinct distribution patterns. The distributions vary site specifically, indicating that different glycoforms of the same protein may have different distributions. Moreover, we comprehensively analyze the dynamics of O-GlcNAcylated and non-modified proteins in these two compartments, respectively, and the half-lives of glycoproteins in different compartments are markedly different, with the median half-life in the cytoplasm being much longer. In addition, glycoproteins in the nucleus are more dramatically stabilized than those in the cytoplasm under the O-GlcNAcase inhibition. The comprehensive spatial and temporal analyses of protein O-GlcNAcylation provide valuable information and advance our understanding of this important modification.
Keywords	GECP: Molecular biology ; CP: Cell biology ; Biology (General) ; QH301-705.5
Subject code	612
Language	English
Publishing date	2022-06-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Oriented Ship Detector for Remote Sensing Imagery Based on Pairwise Branch Detection Head and SAR Feature Enhancement

Bokun He / Qingyi Zhang / Ming Tong / Chu He

Remote Sensing, Vol 14, Iss 2177, p

2022 Volume 2177

Abstract: Recently, object detection in natural images has made a breakthrough, but it is still challenging in oriented ship detection for remote sensing imagery. Considering some limitations in this task, such as uncertain ship orientation, unspecific features ... ...

Abstract	Recently, object detection in natural images has made a breakthrough, but it is still challenging in oriented ship detection for remote sensing imagery. Considering some limitations in this task, such as uncertain ship orientation, unspecific features for locating and classification in the complex optical environment, and multiplicative speckle interference of synthetic aperture radar (SAR), we propose an oriented ship detector based on the pairwise branch detection head and adaptive SAR feature enhancement. The details are as follows: (1) Firstly, the ships with arbitrary directions are described with a rotated ground truth, and an oriented region proposal network (ORPN) is designed to study the transformation from the horizontal region of interest to the rotated region of interest. The ORPN effectively improved the quality of the candidate area while only introducing a few parameters. (2) In view of the existing algorithms that tend to perform classification and regression prediction on the same output feature, this paper proposes a pairwise detection head (PBH) to design parallel branches to decouple classification and locating tasks, so that each branch can learn more task-specific features. (3) Inspired by the ratio-of-average detector in traditional SAR image processing, the SAR edge enhancement (SEE) module is proposed, which adaptively enhances edge pixels, and the threshold of the edge is learned by the channel-shared adaptive thresholds block. Experiments were carried out on both optical and SAR datasets. In the optical dataset, PBH combined with ORPN improved recall by 5.03%, and in the SAR dataset, the overall method achieved a maximum F1 score improvement of 6.07%; these results imply the validity of our method.
Keywords	ship detection ; deep learning ; remote sensing imagery ; SAR feature enhancement ; pairwise head ; Science ; Q
Subject code	600
Language	English
Publishing date	2022-05-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: An Anchor-Free Method Based on Adaptive Feature Encoding and Gaussian-Guided Sampling Optimization for Ship Detection in SAR Imagery

Bokun He / Qingyi Zhang / Ming Tong / Chu He

Remote Sensing, Vol 14, Iss 1738, p

2022 Volume 1738

Abstract: Recently, deep-learning methods have yielded rapid progress for object detection in synthetic aperture radar (SAR) imagery. It is still a great challenge to detect ships in SAR imagery due to ships’ small size and confusable detail feature. This article ... ...

Abstract	Recently, deep-learning methods have yielded rapid progress for object detection in synthetic aperture radar (SAR) imagery. It is still a great challenge to detect ships in SAR imagery due to ships’ small size and confusable detail feature. This article proposes a novel anchor-free detection method composed of two modules to deal with these problems. First, for the lack of detailed information on small ships, we suggest an adaptive feature-encoding module (AFE), which gradually fuses deep semantic features into shallow layers and realizes the adaptive learning of the spatial fusion weights. Thus, it can effectively enhance the external semantics and improve the representation ability of small targets. Next, for the foreground–background imbalance, the Gaussian-guided detection head (GDH) is introduced according to the idea of soft sampling and exploits Gaussian prior to assigning different weights to the detected bounding boxes at different locations in the training optimization. Moreover, the proposed Gauss-ness can down-weight the predicted scores of bounding boxes far from the object center. Finally, the effect of the detector composed of the two modules is verified on the two SAR ship datasets. The results demonstrate that our method can effectively improve the detection performance of small ships in datasets.
Keywords	ship object detection ; deep learning ; remote sensing imagery ; feature extraction ; object sampling ; Science ; Q
Subject code	600
Language	English
Publishing date	2022-04-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Identification of phosphorylation site on PARP1 mediating its cytosolic translocation in virus-infected HeLa cells

Fei Wang / Ming Tong Ma / Junfang Xu / Haipeng Liu

STAR Protocols, Vol 3, Iss 4, Pp 101808- (2022)

2022

Abstract: Summary: Poly (ADP-ribose) polymerase 1 (PARP1) localization is controlled by its phosphorylation state. Here, we describe a protocol to monitor PARP1 subcellular localization in HSV-1-infected HeLa cells using immunofluorescence microscopy and ... ...

Abstract	Summary: Poly (ADP-ribose) polymerase 1 (PARP1) localization is controlled by its phosphorylation state. Here, we describe a protocol to monitor PARP1 subcellular localization in HSV-1-infected HeLa cells using immunofluorescence microscopy and cytoplasmic/nuclear fractionation. We detail steps to identify phosphorylation sites on PARP1 using conserved motif analysis and mass spectrometry. This protocol can be applied to the study of other protein phosphorylation events in other cell types.For complete details on the use and execution of this protocol, please refer to Wang et al. (2022). : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.
Keywords	Cell biology ; Cell separation/fractionation ; Mass spectrometry ; Microscopy ; Molecular biology ; Signal transduction ; Science (General) ; Q1-390
Language	English
Publishing date	2022-12-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Few-Shot Object Detection on Remote Sensing Images via Shared Attention Module and Balanced Fine-Tuning Strategy

Xu Huang / Bokun He / Ming Tong / Dingwen Wang / Chu He

Remote Sensing, Vol 13, Iss 3816, p

2021 Volume 3816

Abstract: Few-shot object detection is a recently emerging branch in the field of computer vision. Recent research studies have proposed several effective methods for object detection with few samples. However, their performances are limited when applied to remote ...

Abstract	Few-shot object detection is a recently emerging branch in the field of computer vision. Recent research studies have proposed several effective methods for object detection with few samples. However, their performances are limited when applied to remote sensing images. In this article, we specifically analyze the characteristics of remote sensing images and propose a few-shot fine-tuning network with a shared attention module (SAM) to adapt to detecting remote sensing objects, which have large size variations. In our SAM, multi-attention maps are computed in the base training stage and shared with the feature extractor in the few-shot fine-tuning stage as prior knowledge to help better locate novel class objects with few samples. Moreover, we design a new few-shot fine-tuning stage with a balanced fine-tuning strategy (BFS), which helps in mitigating the severe imbalance between the number of novel class samples and base class samples caused by the few-shot settings to improve the classification accuracy. We have conducted experiments on two remote sensing datasets (NWPU VHR-10 and DIOR), and the excellent results demonstrate that our method makes full use of the advantages of few-shot learning and the characteristics of remote sensing images to enhance the few-shot detection performance.
Keywords	object detection ; few-shot learning ; remote sensing images ; attention mechanism ; Science ; Q
Subject code	004
Language	English
Publishing date	2021-09-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Computed tomography-based radiomics to predict early recurrence of hepatocellular carcinoma post-hepatectomy in patients background on cirrhosis.

Qian, Gui-Xiang / Xu, Zi-Ling / Li, Yong-Hai / Lu, Jian-Lin / Bu, Xiang-Yi / Wei, Ming-Tong / Jia, Wei-Dong

World journal of gastroenterology

2024 Volume 30, Issue 15, Page(s) 2128–2142

Abstract: Background: The prognosis for hepatocellular carcinoma (HCC) in the presence of cirrhosis is unfavourable, primarily attributable to the high incidence of recurrence.: Aim: To develop a machine learning model for predicting early recurrence (ER) of ... ...

Abstract	Background: The prognosis for hepatocellular carcinoma (HCC) in the presence of cirrhosis is unfavourable, primarily attributable to the high incidence of recurrence. Aim: To develop a machine learning model for predicting early recurrence (ER) of post-hepatectomy HCC in patients with cirrhosis and to stratify patients' overall survival (OS) based on the predicted risk of recurrence. Methods: In this retrospective study, 214 HCC patients with cirrhosis who underwent curative hepatectomy were examined. Radiomics feature selection was conducted using the least absolute shrinkage and selection operator and recursive feature elimination methods. Clinical-radiologic features were selected through univariate and multivariate logistic regression analyses. Five machine learning methods were used for model comparison, aiming to identify the optimal model. The model's performance was evaluated using the receiver operating characteristic curve [area under the curve (AUC)], calibration, and decision curve analysis. Additionally, the Kaplan-Meier (K-M) curve was used to evaluate the stratification effect of the model on patient OS. Results: Within this study, the most effective predictive performance for ER of post-hepatectomy HCC in the background of cirrhosis was demonstrated by a model that integrated radiomics features and clinical-radiologic features. In the training cohort, this model attained an AUC of 0.844, while in the validation cohort, it achieved a value of 0.790. The K-M curves illustrated that the combined model not only facilitated risk stratification but also exhibited significant discriminatory ability concerning patients' OS. Conclusion: The combined model, integrating both radiomics and clinical-radiologic characteristics, exhibited excellent performance in HCC with cirrhosis. The K-M curves assessing OS revealed statistically significant differences.
MeSH term(s)	Humans ; Carcinoma, Hepatocellular/diagnostic imaging ; Carcinoma, Hepatocellular/surgery ; Carcinoma, Hepatocellular/mortality ; Carcinoma, Hepatocellular/pathology ; Liver Neoplasms/diagnostic imaging ; Liver Neoplasms/surgery ; Liver Neoplasms/mortality ; Liver Neoplasms/pathology ; Male ; Female ; Hepatectomy ; Liver Cirrhosis/complications ; Liver Cirrhosis/diagnostic imaging ; Liver Cirrhosis/surgery ; Retrospective Studies ; Middle Aged ; Neoplasm Recurrence, Local/epidemiology ; Aged ; Tomography, X-Ray Computed/methods ; Machine Learning ; Prognosis ; Predictive Value of Tests ; ROC Curve ; Risk Assessment/methods ; Risk Assessment/statistics & numerical data ; Kaplan-Meier Estimate ; Adult ; Liver/diagnostic imaging ; Liver/pathology ; Liver/surgery ; Risk Factors ; Radiomics
Language	English
Publishing date	2024-04-26
Publishing country	United States
Document type	Journal Article
ZDB-ID	2185929-2
ISSN	2219-2840 ; 1007-9327
ISSN (online)	2219-2840
ISSN	1007-9327
DOI	10.3748/wjg.v30.i15.2128
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Article: Risk Factors for Ocular Surface Irritation Symptoms in Inactive Mild and Moderate-to-Severe Graves' Orbitopathy.

Yu, Yun / Hu, Yu-Xin / Lu, Ming-Xi / Ouyang, Zheng-Long / Xu, Ming-Tong / Zhao, Li-Yan / Wang, Mei

Ophthalmology and therapy

2024 Volume 13, Issue 4, Page(s) 1015–1024

Abstract: Introduction: This study aims to analyze risk factors for ocular surface irritation symptoms in patients with non-corneal-damage inactive mild and moderate-to-severe Graves' orbitopathy (GO).: Methods: This retrospective study enrolled 307 patients ... ...

Abstract	Introduction: This study aims to analyze risk factors for ocular surface irritation symptoms in patients with non-corneal-damage inactive mild and moderate-to-severe Graves' orbitopathy (GO). Methods: This retrospective study enrolled 307 patients with non-corneal-damage inactive GO admitted to Sun Yat-sen Memorial Hospital from April 2017 to September 2023. The activity and severity of GO were evaluated using the Clinical Activity Score (CAS) and the European Group on Graves' Orbitopathy (EUGOGO) classification, respectively. Multivariate logistic regression analysis was performed to analyze risk factors for ocular surface irritation symptoms. Results: Among patients with inactive GO, for mild cases, CAS (P < 0.001), upper eyelid lag (P = 0.049), and extraocular muscle involvement (P = 0.019) in the symptomatic group were greater than those in the asymptomatic group, and multivariate logistic regression analysis demonstrated that upper eyelid lag (P = 0.048), CAS 1 (P < 0.001), CAS 2 (P = 0.005), and extraocular muscle involvement (P = 0.029) were risk factors for ocular surface irritation symptoms; for moderate-to-severe cases, CAS (P = 0.004), extraocular muscle involvement (P < 0.001), marginal reflex distance 1 (MRD1) (P = 0.030), and thyroid-stimulating hormone (TSH) (P = 0.034) in the symptomatic group were greater than those in the asymptomatic group, while multivariate logistic regression analysis indicated that extraocular muscle involvement (P = 0.018) and MRD1 (P = 0.012) were risk factors for ocular surface irritation symptoms. Conclusion: In non-corneal-damage inactive mild and moderate-to-severe GO, eyelid malposition and periocular muscle inflammation are risk factors for ocular surface irritation symptoms.
Language	English
Publishing date	2024-02-20
Publishing country	England
Document type	Journal Article
ISSN	2193-8245
ISSN	2193-8245
DOI	10.1007/s40123-024-00892-4
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Identification of phosphorylation site on PARP1 mediating its cytosolic translocation in virus-infected HeLa cells.

Wang, Fei / Ma, Ming Tong / Xu, Junfang / Liu, Haipeng

STAR protocols

2022 Volume 3, Issue 4, Page(s) 101808

Abstract: Poly (ADP-ribose) polymerase 1 (PARP1) localization is controlled by its phosphorylation state. Here, we describe a protocol to monitor PARP1 subcellular localization in HSV-1-infected HeLa cells using immunofluorescence microscopy and cytoplasmic/ ... ...

Abstract	Poly (ADP-ribose) polymerase 1 (PARP1) localization is controlled by its phosphorylation state. Here, we describe a protocol to monitor PARP1 subcellular localization in HSV-1-infected HeLa cells using immunofluorescence microscopy and cytoplasmic/nuclear fractionation. We detail steps to identify phosphorylation sites on PARP1 using conserved motif analysis and mass spectrometry. This protocol can be applied to the study of other protein phosphorylation events in other cell types. For complete details on the use and execution of this protocol, please refer to Wang et al. (2022).
MeSH term(s)	Humans ; HeLa Cells ; Phosphorylation ; Cytosol ; Translocation, Genetic ; Poly (ADP-Ribose) Polymerase-1
Chemical Substances	PARP1 protein, human (EC 2.4.2.30) ; Poly (ADP-Ribose) Polymerase-1 (EC 2.4.2.30)
Language	English
Publishing date	2022-11-02
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	2666-1667
ISSN (online)	2666-1667
DOI	10.1016/j.xpro.2022.101808
Database	MEDical Literature Analysis and Retrieval System OnLINE

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