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Article ; Online: PySNV for complex intra-host variation detection.

Li, Liandong / Fu, Haoyi / Ma, Wentai / Li, Mingkun

2024 Volume 40, Issue 3

Abstract: Motivation: Intra-host variants refer to genetic variations or mutations that occur within an individual host organism. These variants are typically studied in the context of viruses, bacteria, or other pathogens to understand the evolution of pathogens. ...

Abstract	Motivation: Intra-host variants refer to genetic variations or mutations that occur within an individual host organism. These variants are typically studied in the context of viruses, bacteria, or other pathogens to understand the evolution of pathogens. Moreover, intra-host variants are also explored in the field of tumor biology and mitochondrial biology to characterize somatic mutations and inherited heteroplasmic mutations. Intra-host variants can involve long insertions, deletions, and combinations of different mutation types, which poses challenges in their identification. The performance of current methods in detecting of complex intra-host variants is unknown. Results: First, we simulated a dataset comprising 10 samples with 1869 intra-host variants involving various mutation patterns and benchmarked current variant detection software. The results indicated that though current software can detect most variants with F1-scores between 0.76 and 0.97, their performance in detecting long indels and low frequency variants was limited. Thus, we developed a new software, PySNV, for the detection of complex intra-host variations. On the simulated dataset, PySNV successfully detected 1863 variant cases (F1-score: 0.99) and exhibited the highest Pearson correlation coefficient (PCC: 0.99) to the ground truth in predicting variant frequencies. The results demonstrated that PySNV delivered promising performance even for long indels and low frequency variants, while maintaining computational speed comparable to other methods. Finally, we tested its performance on SARS-CoV-2 replicate sequencing data and found that it reported 21% more variants compared to LoFreq, the best-performing benchmarked software, while showing higher consistency (62% over 54%) within replicates. The discrepancies mostly exist in low-depth regions and low frequency variants. Availability and implementation: https://github.com/bnuLyndon/PySNV/.
MeSH term(s)	High-Throughput Nucleotide Sequencing/methods ; Software ; Mutation ; INDEL Mutation ; Genetic Variation
Language	English
Publishing date	2024-03-01
Publishing country	England
Document type	Journal Article
ZDB-ID	1422668-6
ISSN	1367-4811 ; 1367-4803
ISSN (online)	1367-4811
ISSN	1367-4803
DOI	10.1093/bioinformatics/btae116
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Article ; Online: A fast and accurate method for SARS-CoV-2 genomic tracing.

Ma, Wentai / Shi, Leisheng / Li, Mingkun

Briefings in bioinformatics

2023 Volume 24, Issue 6

Abstract: To contain infectious diseases, it is crucial to determine the origin and transmission routes of the pathogen, as well as how the virus evolves. With the development of genome sequencing technology, genome epidemiology has emerged as a powerful approach ... ...

Abstract	To contain infectious diseases, it is crucial to determine the origin and transmission routes of the pathogen, as well as how the virus evolves. With the development of genome sequencing technology, genome epidemiology has emerged as a powerful approach for investigating the source and transmission of pathogens. In this study, we first presented the rationale for genomic tracing of SARS-CoV-2 and the challenges we currently face. Identifying the most genetically similar reference sequence to the query sequence is a critical step in genome tracing, typically achieved using either a phylogenetic tree or a sequence similarity search. However, these methods become inefficient or computationally prohibitive when dealing with tens of millions of sequences in the reference database, as we encountered during the COVID-19 pandemic. To address this challenge, we developed a novel genomic tracing algorithm capable of processing 6 million SARS-CoV-2 sequences in less than a minute. Instead of constructing a giant phylogenetic tree, we devised a weighted scoring system based on mutation characteristics to quantify sequences similarity. The developed method demonstrated superior performance compared to previous methods. Additionally, an online platform was developed to facilitate genomic tracing and visualization of the spatiotemporal distribution of sequences. The method will be a valuable addition to standard epidemiological investigations, enabling more efficient genomic tracing. Furthermore, the computational framework can be easily adapted to other pathogens, paving the way for routine genomic tracing of infectious diseases.
MeSH term(s)	Humans ; SARS-CoV-2/genetics ; COVID-19/epidemiology ; COVID-19/genetics ; Phylogeny ; Pandemics ; Genome, Viral ; Genomics/methods
Language	English
Publishing date	2023-09-22
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2068142-2
ISSN	1477-4054 ; 1467-5463
ISSN (online)	1477-4054
ISSN	1467-5463
DOI	10.1093/bib/bbad339
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Article ; Online: Genomic Analysis of the Suspicious SARS-CoV-2 Sequences in the Public Sequencing Database.

Sun, Xiao / Kan, Chuanwen / Ma, Wentai / Du, Zhenglin / Li, Mingkun

Microbiology spectrum

2023 Volume 11, Issue 1, Page(s) e0342622

Abstract: SARS-CoV-2 has infected more than 600 million people. However, the origin of the virus is still unclear; knowing where the virus came from could help us prevent future zoonotic epidemics. Sequencing data, particularly metagenomic data, can profile the ... ...

Abstract	SARS-CoV-2 has infected more than 600 million people. However, the origin of the virus is still unclear; knowing where the virus came from could help us prevent future zoonotic epidemics. Sequencing data, particularly metagenomic data, can profile the genomes of all species in the sample, including those not recognized at the time, thus allowing for the identification of the progenitor of SARS-CoV-2 in samples collected before the pandemic. We analyzed the data from 5,196 SARS-CoV-2-positive sequencing runs in the NCBI's SRA database with collection dates prior to 2020 or unknown. We found that the mutation patterns obtained from these suspicious SARS-CoV-2 reads did not match the genome characteristics of an unknown progenitor of the virus, suggesting that they may derive from circulating SARS-CoV-2 variants or other coronaviruses. Despite a negative result for tracking the progenitor of SARS-CoV-2, the methods developed in the study could assist in pinpointing the origin of various pathogens in the future.
MeSH term(s)	Humans ; SARS-CoV-2/genetics ; COVID-19 ; Metagenomics ; Mutation ; Genome, Viral
Language	English
Publishing date	2023-01-09
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2807133-5
ISSN	2165-0497 ; 2165-0497
ISSN (online)	2165-0497
ISSN	2165-0497
DOI	10.1128/spectrum.03426-22
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Article ; Online: Immune evasion and ACE2 binding affinity contribute to SARS-CoV-2 evolution.

Ma, Wentai / Fu, Haoyi / Jian, Fanchong / Cao, Yunlong / Li, Mingkun

Nature ecology & evolution

2023 Volume 7, Issue 9, Page(s) 1457–1466

Abstract: Mutations in the SARS-CoV-2 genome could confer resistance to pre-existing antibodies and/or increased transmissibility. The recently emerged Omicron subvariants exhibit a strong tendency for immune evasion, suggesting adaptive evolution. However, ... ...

Abstract	Mutations in the SARS-CoV-2 genome could confer resistance to pre-existing antibodies and/or increased transmissibility. The recently emerged Omicron subvariants exhibit a strong tendency for immune evasion, suggesting adaptive evolution. However, because previous studies have been limited to specific lineages or subsets of mutations, the overall evolutionary trajectory of SARS-CoV-2 and the underlying driving forces are still not fully understood. Here we analysed all open-access SARS-CoV-2 genomes (up to November 2022) and correlated the mutation incidence and fitness changes with the impacts of mutations on immune evasion and ACE2 binding affinity. Our results show that the Omicron lineage had an accelerated mutation rate in the RBD region, while the mutation incidence in other genomic regions did not change dramatically over time. Mutations in the RBD region exhibited a lineage-specific pattern and tended to become more aggregated over time, and the mutation incidence was positively correlated with the strength of antibody pressure. Additionally, mutation incidence was positively correlated with changes in ACE2 binding affinity, but with a lower correlation coefficient than with immune evasion. In contrast, the effect of mutations on fitness was more closely correlated with changes in ACE2 binding affinity than with immune evasion. Our findings suggest that immune evasion and ACE2 binding affinity play significant and diverse roles in the evolution of SARS-CoV-2.
MeSH term(s)	Humans ; Angiotensin-Converting Enzyme 2 ; COVID-19 ; Immune Evasion ; Mutation ; SARS-CoV-2/genetics
Chemical Substances	Angiotensin-Converting Enzyme 2 (EC 3.4.17.23) ; ACE2 protein, human (EC 3.4.17.23)
Language	English
Publishing date	2023-07-13
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	2397-334X
ISSN (online)	2397-334X
DOI	10.1038/s41559-023-02123-8
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Article ; Online: Active Dual-Protein Coating Assisted by Stepwise Protein-Protein Interactions Assembly Reduces Thrombosis and Infection.

Zhang, Wentai / Zhang, Jiangling / Hu, Fangkun / Wang, Wenxuan / Du, Zeyu / Ke, You / Ma, Qing / Mou, Xiaohui / Lu, Jing / Yang, Zhilu

Advanced science (Weinheim, Baden-Wurttemberg, Germany)

2024 , Page(s) e2310259

Abstract: Universal protein coatings have recently gained wide interest in medical applications due to their biocompatibility and ease of fabrication. However, the challenge persists in protein activity preservation, significantly complicating the functional ... ...

Abstract	Universal protein coatings have recently gained wide interest in medical applications due to their biocompatibility and ease of fabrication. However, the challenge persists in protein activity preservation, significantly complicating the functional design of these coatings. Herein, an active dual-protein surface engineering strategy assisted by a facile stepwise protein-protein interactions assembly (SPPIA) method for catheters to reduce clot formation and infection is proposed. This strategy is realized first by the partial oxidation of bovine serum albumin (BSA) and lysozyme (LZM) for creating stable nucleation platforms via hydrophobic interaction, followed by the assembly of nonoxidized BSA (pI, the isoelectric point, ≈4.7) and LZM (pI ≈11) through electrostatic interaction owing to their opposite charge under neutral conditions. The SPPIA method effectively preserves the conformation and functionality of both BSA and LZM, thus endowing the resultant coating with potent antithrombotic and bactericidal properties. Furthermore, the stable nucleation platform ensures the adhesion and durability of the coating, resisting thrombosis and bacterial proliferation even after 15 days of PBS immersion. Overall, the SPPIA approach not only provides a new strategy for the fabrication of active protein coatings but also shows promise for the surface engineering technology of catheters.
Language	English
Publishing date	2024-02-29
Publishing country	Germany
Document type	Journal Article
ZDB-ID	2808093-2
ISSN	2198-3844 ; 2198-3844
ISSN (online)	2198-3844
ISSN	2198-3844
DOI	10.1002/advs.202310259
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Article ; Online: Zwitterionic polymers-armored amyloid-like protein surface combats thrombosis and biofouling.

Mou, Xiaohui / Miao, Wan / Zhang, Wentai / Wang, Wenxuan / Ma, Qing / Du, Zeyu / Li, Xin / Huang, Nan / Yang, Zhilu

Bioactive materials

2023 Volume 32, Page(s) 37–51

Abstract: Proteins, cells and bacteria adhering to the surface of medical devices can lead to thrombosis and infection, resulting in significant clinical mortality. Here, we report a zwitterionic polymers-armored amyloid-like protein surface engineering strategy ... ...

Abstract	Proteins, cells and bacteria adhering to the surface of medical devices can lead to thrombosis and infection, resulting in significant clinical mortality. Here, we report a zwitterionic polymers-armored amyloid-like protein surface engineering strategy we called as "armored-tank" strategy for dual functionalization of medical devices. The "armored-tank" strategy is realized by decoration of partially conformational transformed LZM (PCTL) assembly through oxidant-mediated process, followed by armoring with super-hydrophilic poly-2-methacryloyloxyethyl phosphorylcholine (pMPC). The outer armor of the "armored-tank" shows potent and durable zone defense against fibrinogen, platelet and bacteria adhesion, leading to long-term antithrombogenic properties over 14 days
Language	English
Publishing date	2023-09-27
Publishing country	China
Document type	Journal Article
ISSN	2452-199X
ISSN (online)	2452-199X
DOI	10.1016/j.bioactmat.2023.09.003
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Article ; Online: An insect sclerotization-inspired antifouling armor on biomedical devices combats thrombosis and embedding

Nan Lyu / Daihua Deng / Yuting Xiang / Zeyu Du / Xiaohui Mou / Qing Ma / Nan Huang / Jing Lu / Xin Li / Zhilu Yang / Wentai Zhang

Bioactive Materials, Vol 33, Iss , Pp 562-

2024 Volume 571

Abstract: Thrombus formation and tissue embedding significantly impair the clinical efficacy and retrievability of temporary interventional medical devices. Herein, we report an insect sclerotization-inspired antifouling armor for tailoring temporary ... ...

Abstract	Thrombus formation and tissue embedding significantly impair the clinical efficacy and retrievability of temporary interventional medical devices. Herein, we report an insect sclerotization-inspired antifouling armor for tailoring temporary interventional devices with durable resistance to protein adsorption and the following protein-mediated complications. By mimicking the phenol-polyamine chemistry assisted by phenol oxidases during sclerotization, we develop a facile one-step method to crosslink bovine serum albumin (BSA) with oxidized hydrocaffeic acid (HCA), resulting in a stable and universal BSA@HCA armor. Furthermore, the surface of the BSA@HCA armor, enriched with carboxyl groups, supports the secondary grafting of polyethylene glycol (PEG), further enhancing both its antifouling performance and durability. The synergy of robustly immobilized BSA and covalently grafted PEG provide potent resistance to the adhesion of proteins, platelets, and vascular cells in vitro. In ex vivo blood circulation experiment, the armored surface reduces thrombus formation by 95 %. Moreover, the antifouling armor retained over 60 % of its fouling resistance after 28 days of immersion in PBS. Overall, our armor engineering strategy presents a promising solution for enhancing the antifouling properties and clinical performance of temporary interventional medical devices.
Keywords	Antifouling ; Temporary interventional devices ; Insect sclerotization ; Phenol-polyamine chemistry ; Universal armor ; Materials of engineering and construction. Mechanics of materials ; TA401-492 ; Biology (General) ; QH301-705.5
Language	English
Publishing date	2024-03-01T00:00:00Z
Publisher	KeAi Communications Co., Ltd.
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Glycocalyx-inspired dynamic antifouling surfaces for temporary intravascular devices.

Zhang, Wentai / Cui, Linxian / Xie, Chaoming / Du, Zeyu / Mou, Xiaohui / Ke, You / Ma, Qing / Tian, Wenjie / Yang, Zhilu

Biomaterials

2023 Volume 304, Page(s) 122427

Abstract: Protein and cell adhesion on temporary intravascular devices can lead to thrombosis and tissue embedment, significantly increasing complications and device retrieval difficulties. Here, we propose an endothelial glycocalyx-inspired dynamic antifouling ... ...

Abstract	Protein and cell adhesion on temporary intravascular devices can lead to thrombosis and tissue embedment, significantly increasing complications and device retrieval difficulties. Here, we propose an endothelial glycocalyx-inspired dynamic antifouling surface strategy for indwelling catheters and retrievable vascular filters to prevent thrombosis and suppress intimal embedment. This strategy is realized on the surfaces of substrates by the intensely dense grafting of hydrolyzable endothelial polysaccharide hyaluronic acid (HA), assisted by an amine-rich phenol-polyamine universal platform. The resultant super-hydrophilic surface exhibits potent antifouling property against proteins and cells. Additionally, the HA hydrolysis induces continuous degradation of the coating, enabling removal of inevitable biofouling on the surface. Moreover, the dense grafting of HA also ensures the medium-term effectiveness of this dynamic antifouling surface. The coated catheters maintain a superior anti-thrombosis capacity in ex vivo blood circulation after 30 days immersion. In the abdominal veins of rats, the coated implants show inhibitory effects on intimal embedment up to 2 months. Overall, we envision that this glycocalyx-inspired dynamic antifouling surface strategy could be a promising surface engineering technology for temporary intravascular devices.
MeSH term(s)	Rats ; Animals ; Biofouling/prevention & control ; Proteins ; Hyaluronic Acid/chemistry ; Hydrophobic and Hydrophilic Interactions ; Thrombosis/prevention & control ; Surface Properties
Chemical Substances	Proteins ; Hyaluronic Acid (9004-61-9)
Language	English
Publishing date	2023-12-11
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	603079-8
ISSN	1878-5905 ; 0142-9612
ISSN (online)	1878-5905
ISSN	0142-9612
DOI	10.1016/j.biomaterials.2023.122427
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Article ; Online: Effects of organic fertilizer addition on field phosphorus status and yield under different amounts of phosphorus fertilization in cotton field in Xinjiang, China

YUAN Fang / ZHANG Kai / MA Chao / ZHANG Nan / SHENG Jiandong / ZHANG Wentai

Journal of Agricultural Resources and Environment, Vol 39, Iss 1, Pp 118-

2022 Volume 128

Abstract: This research aimed to study the effect of different phosphorus fertilizer rates and organic fertilizer addition on the soil phosphorus availability, plant uptake and distribution, yield composition, and field phosphorus balance of cotton fields in ... ...

Abstract	This research aimed to study the effect of different phosphorus fertilizer rates and organic fertilizer addition on the soil phosphorus availability, plant uptake and distribution, yield composition, and field phosphorus balance of cotton fields in Xinjiang, which would help increase phosphate fertilizer use efficiency and the sustainable phosphate management of cotton field in Xinjiang. Different phosphorus fertilization rate treatments(0, 50, 100 kg·hm-2, and 150 kg·hm-2), with and without organic fertilizer(organic fertilizer 4 500 kg · hm-2)were set under the field conditions. The contents of soil-available phosphorus and plant uptake, distribution, and yield were measured. The phosphate fertilizer use efficiency and field phosphorus balance were calculated. Results showed that: soil-available phosphorus showed an increasing tendency with the increase of phosphorus fertilization rate; soil-available phosphorus content in the treatment with organic fertilizer was higher than that in the treatment without organic fertilizer. The plants ′ accumulated phosphorus uptake showed an increasing trend, with the highest value found at 150 kg·hm-2. With the increase of phosphorus application, the seed cotton yield first increased and then slightly decreased. The yield of the treatment with organic fertilizer was generally greater than that of the treatment without organic fertilizer. The seed cotton yield was highest(5 642 kg · hm-2)at 100 kg · hm-2 when organic fertilizers were added. The phosphate fertilizer recovery rate was optimal(37.24%)at 100 kg·hm-2. With the increase of phosphorus fertilization rate, field phosphorus surplus showed an increasing trend, with the first positive value found at 100 kg·hm-2(16.82 kg·hm-2). Organic fertilizer addition under a reduced phosphorus fertilizer application condition could change soil phosphorus availability and plant uptake, distribution, and seed cotton yield. Based on soil phosphorus availability, plant phosphorus uptake and distribution, yield and field phosphorus balance, it is recommended to add 100 kg·hm-2 organic fertilizer base on proper phosphorus fertilization rates in Xinjiang cotton fields.
Keywords	organic fertilizers ; cotton ; plant uptake ; phosphorus fertilization rate ; Agriculture (General) ; S1-972 ; Environmental sciences ; GE1-350
Language	Chinese
Publishing date	2022-01-01T00:00:00Z
Publisher	Agro-Environmental Protection Institute, Ministry of Agriculture
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Correction: Transcriptional and physiological analyses of reduced density in apple provide insight into the regulation involved in photosynthesis.

Niu, Junqiang / Ma, Ming / Yin, Xiaoning / Liu, Xinglu / Dong, Tie / Sun, Wentai / Yang, Fuxia

PloS one

2020 Volume 15, Issue 12, Page(s) e0244012

Abstract: This corrects the article DOI: 10.1371/journal.pone.0239737.]. ...

Abstract	[This corrects the article DOI: 10.1371/journal.pone.0239737.].
Language	English
Publishing date	2020-12-09
Publishing country	United States
Document type	Published Erratum
ISSN	1932-6203
ISSN (online)	1932-6203
DOI	10.1371/journal.pone.0244012
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