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Article ; Online: Computational investigation of the inhibitory interaction of IRF3 and SARS-CoV-2 accessory protein ORF3b.

Bai, Ganggang / Zeng, Xincheng / Zhang, Linghao / Wang, Yanjing / Ma, Buyong

Biochemical and biophysical research communications

2024 Volume 712-713, Page(s) 149945

Abstract: ORF3b is one of the SARS-CoV-2 accessory proteins. Previous experimental study suggested that ORF3b prevents IRF3 translocating to nucleus. However, the biophysical mechanism of ORF3b-IRF3 interaction is elusive. Here, we explored the conformation ... ...

Abstract	ORF3b is one of the SARS-CoV-2 accessory proteins. Previous experimental study suggested that ORF3b prevents IRF3 translocating to nucleus. However, the biophysical mechanism of ORF3b-IRF3 interaction is elusive. Here, we explored the conformation ensemble of ORF3b using all-atom replica exchange molecular dynamics simulation. Disordered ORF3b has mixed α-helix, β-turn and loop conformers. The potential ORF3b-IRF3 binding modes were searched by docking representative ORF3b conformers with IRF3, and 50 ORF3b-IRF3 complex poses were screened using molecular dynamics simulations ranging from 500 to 1000 ns. We found that ORF3b binds IRF3 predominantly on its CBP binding and phosphorylated pLxIS motifs, with CBP binding site has the highest binding affinity. The ORF3b-IRF3 binding residues are highly conserved in SARS-CoV-2. Our results provided biophysics insights into ORF3b-IRF3 interaction and explained its interferon antagonism mechanism.
MeSH term(s)	Interferon Regulatory Factor-3/metabolism ; Interferon Regulatory Factor-3/chemistry ; SARS-CoV-2/metabolism ; SARS-CoV-2/chemistry ; Molecular Dynamics Simulation ; Humans ; Protein Binding ; Binding Sites ; COVID-19/virology ; COVID-19/metabolism ; Molecular Docking Simulation ; Viral Regulatory and Accessory Proteins/metabolism ; Viral Regulatory and Accessory Proteins/chemistry ; Protein Conformation
Chemical Substances	Interferon Regulatory Factor-3 ; IRF3 protein, human ; Viral Regulatory and Accessory Proteins
Language	English
Publishing date	2024-04-16
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	205723-2
ISSN	1090-2104 ; 0006-291X ; 0006-291X
ISSN (online)	1090-2104 ; 0006-291X
ISSN	0006-291X
DOI	10.1016/j.bbrc.2024.149945
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Zs.A 116: Show issues

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Article ; Online: Recent Progress in Antibody Epitope Prediction.

Zeng, Xincheng / Bai, Ganggang / Sun, Chuance / Ma, Buyong

Antibodies (Basel, Switzerland)

2023 Volume 12, Issue 3

Abstract: Recent progress in epitope prediction has shown promising results in the development of vaccines and therapeutics against various diseases. However, the overall accuracy and success rate need to be improved greatly to gain practical application ... ...

Abstract	Recent progress in epitope prediction has shown promising results in the development of vaccines and therapeutics against various diseases. However, the overall accuracy and success rate need to be improved greatly to gain practical application significance, especially conformational epitope prediction. In this review, we examined the general features of antibody-antigen recognition, highlighting the conformation selection mechanism in flexible antibody-antigen binding. We recently highlighted the success and warning signs of antibody epitope predictions, including linear and conformation epitope predictions. While deep learning-based models gradually outperform traditional feature-based machine learning, sequence and structure features still provide insight into antibody-antigen recognition problems.
Language	English
Publishing date	2023-08-08
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2661514-9
ISSN	2073-4468 ; 2073-4468
ISSN (online)	2073-4468
ISSN	2073-4468
DOI	10.3390/antib12030052
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Acyl-CoA-binding protein (ACBP) genes involvement in response to abiotic stress and exogenous hormone application in barley (Hordeum vulgare L.).

Chang, Huayu / Ma, Minhu / Gu, Mingzhou / Li, Shanshan / Li, Mengrun / Guo, Ganggang / Xing, Guofang

BMC plant biology

2024 Volume 24, Issue 1, Page(s) 236

Abstract: Background: Acyl-CoA-Binding proteins (ACBPs) function as coenzyme A transporters and play important roles in regulating plant growth and development in response to abiotic stress and phytohormones, as well as in membrane repair. To date, the ACBP ... ...

Abstract	Background: Acyl-CoA-Binding proteins (ACBPs) function as coenzyme A transporters and play important roles in regulating plant growth and development in response to abiotic stress and phytohormones, as well as in membrane repair. To date, the ACBP family has not been a comprehensively characterized in barley (Hordeum vulgare L.). Results: Eight ACBP genes were identified in the barley genome and named as HvACBP1-8. The analysis of the proteins structure and promoter elements of HvACBP suggested its potential functions in plant growth, development, and stress response. These HvACBPs are expressed in specific tissues and organs following induction by abiotic stressors such as drought, salinity, UV-B exposure, temperature extremes, and exposure to exogenous phytohormones. The HvACBP7 and HvACBP8 amino acid sequences were conserved during the domestication of Tibetan Qingke barley. Conclusions: Acyl-CoA-binding proteins may play important roles in barley growth and environmental adaptation. This study provides foundation for further analyses of the biological functions of HvACBPs in the barley stress response.
MeSH term(s)	Hordeum/genetics ; Hordeum/metabolism ; Diazepam Binding Inhibitor/metabolism ; Plant Growth Regulators ; Hormones ; Stress, Physiological/genetics
Chemical Substances	Diazepam Binding Inhibitor ; Plant Growth Regulators ; Hormones
Language	English
Publishing date	2024-04-02
Publishing country	England
Document type	Journal Article
ZDB-ID	2059868-3
ISSN	1471-2229 ; 1471-2229
ISSN (online)	1471-2229
ISSN	1471-2229
DOI	10.1186/s12870-024-04944-6
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Article ; Online: Evaluation of Molecular Simulations and Deep Learning Prediction of Antibodies' Recognition of TRBC1 and TRBC2.

Zeng, Xincheng / Wang, Tianqun / Kang, Yue / Bai, Ganggang / Ma, Buyong

Antibodies (Basel, Switzerland)

2023 Volume 12, Issue 3

Abstract: T cell receptor β-chain constant (TRBC) is a promising class of cancer targets consisting of two highly homologous proteins, TRBC1 and TRBC2. Developing targeted antibody therapeutics against TRBC1 or TRBC2 is expected to eradicate the malignant T cells ... ...

Abstract	T cell receptor β-chain constant (TRBC) is a promising class of cancer targets consisting of two highly homologous proteins, TRBC1 and TRBC2. Developing targeted antibody therapeutics against TRBC1 or TRBC2 is expected to eradicate the malignant T cells and preserve half of the normal T cells. Recently, several antibody engineering strategies have been used to modulate the TRBC1 and TRBC2 specificity of antibodies. Here, we used molecular simulation and artificial intelligence methods to quantify the affinity difference in antibodies with various mutations for TRBC1 and TRBC2. The affinity of the existing mutants was verified by FEP calculations aided by the AI. We also performed long-time molecular dynamics simulations to reveal the dynamical antigen recognition mechanisms of the TRBC antibodies.
Language	English
Publishing date	2023-09-17
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2661514-9
ISSN	2073-4468 ; 2073-4468
ISSN (online)	2073-4468
ISSN	2073-4468
DOI	10.3390/antib12030058
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Article ; Online: miR-147b is an oncomiR acting synergistically with HIPK2 to promote pancreatic carcinogenesis.

Wang, Ganggang / Ma, Zenghui / Song, Chao / Wang, Xiaoliang / Zhou, Zhijie

Cellular signalling

2023 Volume 111, Page(s) 110840

Abstract: MicroRNAs (miRs, miRNAs) are known players in the regulatory network of pancreatic tumorigenesis, but the downstream effectors remain poorly characterized. This study addressed this issue based on in silico prediction, in vitro experiments, and in vivo ... ...

Abstract	MicroRNAs (miRs, miRNAs) are known players in the regulatory network of pancreatic tumorigenesis, but the downstream effectors remain poorly characterized. This study addressed this issue based on in silico prediction, in vitro experiments, and in vivo validation. The differentially expressed PCa-related miRNAs and bioinformatics tools predicted downstream regulators. The expression of miR-147b was examined in PCa cell lines. Putative targets of miR-147b were predicted by a publicly available database and confirmed by luciferase activity assay. Mimic/inhibitor, siRNA/overexpression plasmid, or pifithrin-α (p53 inhibitor) were delivered into PCa cells to assess the effect of miR-147b, HIPK2, and p53 on malignant phenotypes of PCa cells. AntagomiR-147b and shRNA targeting HIPK2 were introduced to xenograft-bearing nude mice for in vivo experiments. The expression of miR-147b was significantly increased in PCa cell lines. Ectopic expression of miR-147b promoted the malignant phenotypes of PCa cells and inhibited their apoptosis. HIPK2 was confirmed as a target gene of miR-147b. Inhibiting miR-147b could promote HIPK2 expression and potentially activate the p53 pathway, inhibiting PCa cell growth. In vivo experiments suggested that miR-147b inhibition suppressed the growth of xenograft tumors in nude mice, while HIPK2 knockdown counteracted its effect. Collectively, our work reveals a novel miR-147b-mediated carcinogenic regulatory network in PCa that may be a viable target for PCa treatment.
MeSH term(s)	Humans ; Animals ; Mice ; Mice, Nude ; Tumor Suppressor Protein p53/genetics ; Tumor Suppressor Protein p53/metabolism ; MicroRNAs/metabolism ; Cell Line ; Cell Proliferation/genetics ; Carcinogenesis/genetics ; Cell Line, Tumor ; Gene Expression Regulation, Neoplastic ; Carrier Proteins/genetics ; Carrier Proteins/metabolism ; Protein Serine-Threonine Kinases/genetics ; Protein Serine-Threonine Kinases/metabolism
Chemical Substances	Tumor Suppressor Protein p53 ; MicroRNAs ; HIPK2 protein, human (EC 2.7.1.-) ; Carrier Proteins ; Protein Serine-Threonine Kinases (EC 2.7.11.1)
Language	English
Publishing date	2023-08-03
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1002702-6
ISSN	1873-3913 ; 0898-6568
ISSN (online)	1873-3913
ISSN	0898-6568
DOI	10.1016/j.cellsig.2023.110840
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Zs.A 2579: Show issues

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bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
Jg. 1995 - 2021: Lesesall (2.OG)
ab Jg. 2022: Lesesaal (EG)

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Article ; Online: Stabilized Li-Rich Layered Oxide Cathode by a Spontaneously Formed Yb and Oxygen-Vacancy Rich Layer on the Surface.

Li, Quan / Wang, Hong / Wang, Guan / Xia, Fanjie / Zeng, Weihao / Peng, Haoyang / Ma, Ganggang / Guo, Anan / Dong, Ruifeng / Wu, Jinsong

Small (Weinheim an der Bergstrasse, Germany)

2023 Volume 20, Issue 8, Page(s) e2307419

Abstract: Li-rich layered oxides (LLOs) are among the most promising cathode materials with high theoretical specific capacity (>250 mAh ... ...

Abstract	Li-rich layered oxides (LLOs) are among the most promising cathode materials with high theoretical specific capacity (>250 mAh g
Language	English
Publishing date	2023-10-11
Publishing country	Germany
Document type	Journal Article
ZDB-ID	2168935-0
ISSN	1613-6829 ; 1613-6810
ISSN (online)	1613-6829
ISSN	1613-6810
DOI	10.1002/smll.202307419
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: CoreSNP: an efficient pipeline for core marker profile selection from genome-wide SNP datasets in crops.

Dou, Tingyu / Wang, Chunchao / Ma, Yanling / Chen, Zhaoyan / Zhang, Jing / Guo, Ganggang

BMC plant biology

2023 Volume 23, Issue 1, Page(s) 580

Abstract: Background: DNA marker profiles play a crucial role in the identification and registration of germplasm, as well as in the distinctness, uniformity, and stability (DUS) testing of new plant variety protection. However, selecting minimal marker sets from ...

Abstract	Background: DNA marker profiles play a crucial role in the identification and registration of germplasm, as well as in the distinctness, uniformity, and stability (DUS) testing of new plant variety protection. However, selecting minimal marker sets from large-scale SNP dataset can be challenging to distinguish a maximum number of samples. Results: Here, we developed the CoreSNP pipeline using a "divide and conquer" strategy and a "greedy" algorithm. The pipeline offers adjustable parameters to guarantee the distinction of each sample pair with at least two markers. Additionally, it allows datasets with missing loci as input. The pipeline was tested in barley, soybean, wheat, rice and maize. A few dozen of core SNPs were efficiently selected in different crops with SNP array, GBS, and WGS dataset, which can differentiate thousands of individual samples. The core SNPs were distributed across all chromosomes, exhibiting lower pairwise linkage disequilibrium (LD) and higher polymorphism information content (PIC) and minor allele frequencies (MAF). It was shown that both the genetic diversity of the population and the characteristics of the original dataset can significantly influence the number of core markers. In addition, the core SNPs capture a certain level of the original population structure. Conclusions: CoreSNP is an efficiency way of core marker sets selection based on Genome-wide SNP datasets of crops. Combined with low-density SNP chip or genotyping technologies, it can be a cost-effective way to simplify and expedite the evaluation of genetic resources and differentiate different crop varieties. This tool is expected to have great application prospects in the rapid comparison of germplasm and intellectual property protection of new varieties.
MeSH term(s)	Genotype ; Polymorphism, Single Nucleotide/genetics ; Genome, Plant ; Linkage Disequilibrium/genetics ; Genetic Markers ; Crops, Agricultural/genetics
Chemical Substances	Genetic Markers
Language	English
Publishing date	2023-11-21
Publishing country	England
Document type	Journal Article
ZDB-ID	2059868-3
ISSN	1471-2229 ; 1471-2229
ISSN (online)	1471-2229
ISSN	1471-2229
DOI	10.1186/s12870-023-04609-w
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Article ; Online: AQP3-mediated activation of the AMPK/SIRT1 signaling pathway curtails gallstone formation in mice by inhibiting inflammatory injury of gallbladder mucosal epithelial cells.

Wang, Ganggang / Zhang, Hao / Zhou, Zhijie / Jin, Wenzhi / Zhang, Xin / Ma, Zenghui / Wang, Xiaoliang

Molecular medicine (Cambridge, Mass.)

2023 Volume 29, Issue 1, Page(s) 116

Abstract: Background: Inflammatory injury of gallbladder mucosal epithelial cells affects the development of cholelithiasis, and aquaporin 3 (AQP3) is an important regulator of inflammatory response. This study reports a mechanistic insight into AQP3 regulating ... ...

Abstract	Background: Inflammatory injury of gallbladder mucosal epithelial cells affects the development of cholelithiasis, and aquaporin 3 (AQP3) is an important regulator of inflammatory response. This study reports a mechanistic insight into AQP3 regulating gallstone formation in cholelithiasis based on high-throughput sequencing. Methods: A mouse model of cholelithiasis was induced using a high-fat diet, and the gallbladder tissues were harvested for high-throughput sequencing to obtain differentially expressed genes. Primary mouse gallbladder mucosal epithelial cells were isolated and induced with Lipopolysaccharides (LPS) to mimic an in vitro inflammatory injury environment. Cell biological phenotypes were detected by TdT-mediated dUTP Nick-End Labeling (TUNEL) assay, flow cytometry, Cell Counting Kit-8 (CCK-8) assay, and Trypan blue staining. In addition, enzyme linked immunosorbent assay (ELISA) determined the production of inflammatory factors in mouse gallbladder mucosa. Results: Whole-transcriptome sequencing data analysis identified 489 up-regulated and 1007 down-regulated mRNAs. Bioinformatics analysis revealed that AQP3 was significantly down-regulated in mice with cholelithiasis. AQP3 might also confer an important role in LPS-induced gallbladder mucosal injury. Overexpression of AQP3 activated the AMPK (adenosine monophosphate-activated protein kinase) / SIRT1 (sirtuin-1) signaling pathway to reduce LPS-induced inflammatory injury of the gallbladder mucosa epithelium, thereby ameliorating gallbladder damage and repressing gallstone formation in mice. Conclusion: Data from our study highlight the inhibitory role of AQP3 in gallbladder damage and gallstone formation in mice by reducing inflammatory injury of gallbladder mucosal epithelial cells, which is achieved through activation of the AMPK/SIRT1 signaling pathway.
MeSH term(s)	Animals ; Mice ; Gallstones ; AMP-Activated Protein Kinases ; Aquaporin 3 ; Sirtuin 1/genetics ; Lipopolysaccharides ; Epithelial Cells ; Mucous Membrane ; Signal Transduction
Chemical Substances	AMP-Activated Protein Kinases (EC 2.7.11.31) ; Aquaporin 3 (158801-98-0) ; Sirtuin 1 (EC 3.5.1.-) ; Lipopolysaccharides
Language	English
Publishing date	2023-08-28
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1283676-x
ISSN	1528-3658 ; 1076-1551
ISSN (online)	1528-3658
ISSN	1076-1551
DOI	10.1186/s10020-023-00712-8
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Zs.A 4456: Show issues

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bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
Jg. 1995 - 2021: Lesesall (2.OG)
ab Jg. 2022: Lesesaal (EG)

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Article ; Online: Span-based model for overlapping entity recognition and multi-relations classification in the food domain.

Zhang, Mengqi / Ma, Lei / Ren, Yanzhao / Zhang, Ganggang / Liu, Xinliang

Mathematical biosciences and engineering : MBE

2022 Volume 19, Issue 5, Page(s) 5134–5152

Abstract: Information extraction (IE) is an important part of the entire knowledge graph lifecycle. In the food domain, extracting information such as ingredient and cooking method from Chinese recipes is crucial to safety risk analysis and identification of ... ...

Abstract	Information extraction (IE) is an important part of the entire knowledge graph lifecycle. In the food domain, extracting information such as ingredient and cooking method from Chinese recipes is crucial to safety risk analysis and identification of ingredient. In comparison with English, due to the complex structure, the richness of information in word combination, and lack of tense, Chinese IE is much more challenging. This dilemma is particularly prominent in the food domain with high-density knowledge, imprecise syntactic structure. However, existing IE methods focus only on the features of entities in a sentence, such as context and position, and ignore features of the entity itself and the influence of self attributes on prediction of inter entity relationship. To solve the problems of overlapping entity recognition and multi-relations classification in the food domain, we propose a span-based model known as SpIE for IE. The SpIE uses the span representation for each possible candidate entity to capture span-level features, which transforms named entity recognition (NER) into a classification mission. Besides, SpIE feeds extra information about the entity into the relation classification (RC) model by considering the effect of entity's attributes (both the entity mention and entity type) on the relationship between entity pairs. We apply SpIE on two datasets and observe that SpIE significantly outperforms the previous neural approaches due to capture the feature of overlapping entity and entity attributes, and it remains very competitive in general IE.
MeSH term(s)	Information Storage and Retrieval ; Language ; Research Design ; Risk Assessment
Language	English
Publishing date	2022-04-16
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2265126-3
ISSN	1551-0018 ; 1551-0018
ISSN (online)	1551-0018
ISSN	1551-0018
DOI	10.3934/mbe.2022240
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Correction: USP53 plays an antitumor role in hepatocellular carcinoma through deubiquitination of cytochrome c.

Yao, Ye / Ma, Weijie / Guo, Yonghua / Liu, Yingyi / Xia, Peng / Wu, Xiaoling / Chen, Yiran / Wang, Kunlei / Mei, Chengjie / Wang, Ganggang / Li, Xiaomian / Zhang, Zhonglin / Chen, Xi / Yuan, Yufeng

Oncogenesis

2023 Volume 12, Issue 1, Page(s) 27

Language	English
Publishing date	2023-05-15
Publishing country	United States
Document type	Published Erratum
ZDB-ID	2674437-5
ISSN	2157-9024
ISSN	2157-9024
DOI	10.1038/s41389-023-00470-6
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