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Article: Phage-Derived Depolymerase: Its Possible Role for Secondary Bacterial Infections in COVID-19 Patients.

Nazir, Amina / Song, Jiaoyang / Chen, Yibao / Liu, Yuqing

2023 Volume 11, Issue 2

Abstract: As of 29 July 2022, there had been a cumulative 572,239,451 confirmed cases of COVID-19 worldwide, including 6,390,401 fatalities. COVID-19 patients with severe symptoms are usually treated with a combination of virus- and drug-induced immuno-suppression ...

Abstract	As of 29 July 2022, there had been a cumulative 572,239,451 confirmed cases of COVID-19 worldwide, including 6,390,401 fatalities. COVID-19 patients with severe symptoms are usually treated with a combination of virus- and drug-induced immuno-suppression medicines. Critical clinical complications of the respiratory system due to secondary bacterial infections (SBIs) could be the reason for the high mortality rate in COVID-19 patients. Unfortunately, antimicrobial resistance is increasing daily, and only a few options are available in our antimicrobial armory. Hence, alternative therapeutic options such as enzymes derived from bacteriophages can be considered for treating SBIs in COVID-19 patients. In particular, phage-derived depolymerases have high antivirulent potency that can efficiently degrade bacterial capsular polysaccharides, lipopolysaccharides, and exopolysaccharides. They have emerged as a promising class of new antibiotics and their therapeutic role for bacterial infections is already confirmed in animal models. This review provides an overview of the rising incidence of SBIs among COVID-19 patients. We present a practicable novel workflow for phage-derived depolymerases that can easily be adapted for treating SBIs in COVID-19 patients.
Language	English
Publishing date	2023-02-07
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2720891-6
ISSN	2076-2607
ISSN	2076-2607
DOI	10.3390/microorganisms11020424
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Article ; Online: Disarm The Bacteria: What Temperate Phages Can Do.

Zhou, Shiyue / Liu, Zhengjie / Song, Jiaoyang / Chen, Yibao

Current issues in molecular biology

2023 Volume 45, Issue 2, Page(s) 1149–1167

Abstract: In the field of phage applications and clinical treatment, virulent phages have been in the spotlight whereas temperate phages received, relatively speaking, less attention. The fact that temperate phages often carry virulent or drug-resistant genes is a ...

Abstract	In the field of phage applications and clinical treatment, virulent phages have been in the spotlight whereas temperate phages received, relatively speaking, less attention. The fact that temperate phages often carry virulent or drug-resistant genes is a constant concern and drawback in temperate phage applications. However, temperate phages also play a role in bacterial regulation. This review elucidates the biological properties of temperate phages based on their life cycle and introduces the latest work on temperate phage applications, such as on host virulence reduction, biofilm degradation, genetic engineering and phage display. The versatile use of temperate phages coupled with their inherent properties, such as economy, ready accessibility, wide variety and host specificity, make temperate phages a solid candidate in tackling bacterial infections.
Language	English
Publishing date	2023-02-01
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2000024-8
ISSN	1467-3045 ; 1467-3037
ISSN (online)	1467-3045
ISSN	1467-3037
DOI	10.3390/cimb45020076
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Article ; Online: Feature-weight based measurement of cancerous transcriptome using cohort-wide and sample-specific information.

Wang, Qilu / Song, Jiaoyang Jessie / Zhang, Feng

Cellular oncology (Dordrecht)

2023 Volume 47, Issue 2, Page(s) 711–715

Abstract: Identifying cancerous samples or cells using transcriptomic data is critical for cancer related basic research, early diagnosis, and targeted therapy. However, the high transcriptional heterogeneity of cancers still hinders people from accurately ... ...

Abstract	Identifying cancerous samples or cells using transcriptomic data is critical for cancer related basic research, early diagnosis, and targeted therapy. However, the high transcriptional heterogeneity of cancers still hinders people from accurately recognizing cancerous transcriptome using bulk, single-cell, or spatial RNA-seq data. Here, we present a novel method named FWP (Feature Weight Pro) that helps measure cancerous transcriptome using transcriptomic data. The workflow of FWP is, first, to calculate feature weights using the training dataset, and then, for each sample in the testing dataset, calculate the feature-weight based final score by combining the cohort-wide and sample-specific information. Those two types of information are utilized through conducting weighted principal component analysis and calculating correlation perturbations. The effectiveness and superiority of FWP over other methods are shown by using bulk, single-cell, and spatial RNA-seq data of multiple cancer types. In addition, the high robustness and efficiency of FWP are also demonstrated by using different numbers of features and cells, respectively. FWP is available at https://github.com/jumphone/fwp .
MeSH term(s)	Humans ; Neoplasms/genetics ; Transcriptome/genetics ; Gene Expression Profiling/methods ; Principal Component Analysis ; Cohort Studies ; Gene Expression Regulation, Neoplastic ; Algorithms ; Single-Cell Analysis/methods
Language	English
Publishing date	2023-10-09
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	2595109-9
ISSN	2211-3436 ; 1875-8606 ; 2211-3428
ISSN (online)	2211-3436
ISSN	1875-8606 ; 2211-3428
DOI	10.1007/s13402-023-00879-6
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Article ; Online: Phage Engineering for Targeted Multidrug-Resistant

Song, Jiaoyang / Liu, Zhengjie / Zhang, Qing / Liu, Yuqing / Chen, Yibao

International journal of molecular sciences

2023 Volume 24, Issue 3

Abstract: The lytic bacteriophages have potential application value in the treatment of bacterial infections. However, the narrow host spectrum of these phages limits their range of clinical application. Here, we demonstrate the use of scarless Cas9-assisted ... ...

Abstract	The lytic bacteriophages have potential application value in the treatment of bacterial infections. However, the narrow host spectrum of these phages limits their range of clinical application. Here, we demonstrate the use of scarless Cas9-assisted recombination (no-SCAR) gene-editing technology to regulate phage-host range. We used phage PHB20 as the scaffold to create agents targeting different multidrug-resistant
MeSH term(s)	Bacteriophages/genetics ; Escherichia coli/genetics ; Gene Editing ; Bacteria/genetics ; Drug Resistance, Multiple, Bacterial/genetics
Language	English
Publishing date	2023-01-27
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms24032459
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Article ; Online: Size Effect of TiO2 Nanoparticles as Food Additive and Potential Toxicity

Lü, Naiyan / Chen, Zhe / Song, Jiaoyang / Weng, Yuyan / Yang, Guofeng / Liu, Qingrun / Yang, Kai / Lü, Xuemei / Liu, Yu

Food biophysics. 2022 Mar., v. 17, no. 1 p.75-83

2022

Abstract: Titanium dioxide (TiO₂), as a representative of metallic oxides, is widely used as food additive to serve as coloring or antibacterial packaging fortifier. However, in recent years, the potential hazards of nano-sized TiO₂ food additives to human beings ... ...

Abstract	Titanium dioxide (TiO₂), as a representative of metallic oxides, is widely used as food additive to serve as coloring or antibacterial packaging fortifier. However, in recent years, the potential hazards of nano-sized TiO₂ food additives to human beings is still in doubt. In this work, we systematically studied the interactions between three sizes of TiO₂ particles and the cell membrane systems with confocal laser scanning microscopy. We used both giant unilamellar vesicles and human colon cancer cells to mimic actual cell membrane systems. The results demonstrate the strong effect of particle size on membrane disruption and leakage behaviors. Among the three sizes of TiO₂ nanoparticles (NPs) used in this work, the TiO₂ NPs with the size of 110-300 nm are safe. In contrast, NPs with the size of 10-30 nm and 50-100 nm will cause the rupture and leakage of cell membranes. These indicates that the cytotoxicity of nano-sized TiO₂ particles increases with the decrease of particle sizes. In addition, it is found that the size effect of TiO₂ particles further depends on the membrane charge state. Simulations were also introduced to understand the results. This study would provide a theoretical basis for the production designing and safety standard of metallic oxide food additives.
Keywords	biophysics ; cell membranes ; colorectal neoplasms ; cytotoxicity ; food additives ; humans ; particle size ; titanium dioxide
Language	English
Dates of publication	2022-03
Size	p. 75-83.
Publishing place	Springer US
Document type	Article ; Online
ZDB-ID	2238029-2
ISSN	1557-1866 ; 1557-1858
ISSN (online)	1557-1866
ISSN	1557-1858
DOI	10.1007/s11483-021-09695-7
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Article: Characterisation of a newly detected bacteriophage infecting Bordetella bronchiseptica in swine

Chen, Yibao / Yang, Lan / Sun, Erchao / Song, Jiaoyang / Wu, Bin

Archives of virology. 2019 Jan., v. 164, no. 1

2019

Abstract: A novel virulent bacteriophage, vB_BbrM_PHB04, infecting Bordetella bronchiseptica was isolated from wastewater collected at a swine farm in China. Phage vB_BbrM_PHB04 exhibited growth over a wide range of temperature and pH conditions and showed ... ...

Abstract	A novel virulent bacteriophage, vB_BbrM_PHB04, infecting Bordetella bronchiseptica was isolated from wastewater collected at a swine farm in China. Phage vB_BbrM_PHB04 exhibited growth over a wide range of temperature and pH conditions and showed different efficiency of plating values and lytic spectra within the same strains at 25 °C and 37 °C. High-throughput sequencing revealed that vB_BbrM_PHB04 has a linear double-stranded DNA genome with 124 putative open reading frames. Overall, the genome of vB_BbrM_PHB04 showed very low similarity (the highest nucleotide identity 82%, 1% coverage) to other phage sequences in the GenBank database. Phylogenetic analysis indicated that vB_BbrM_PHB04 is a new member of the family Myoviridae. In addition, polymerase chain reaction-based detection of phage genes in phage-resistant B. bronchiseptica variants revealed no evidence of lysogenic activity of phage vB_BbrM_PHB04.
Keywords	Bordetella bronchiseptica ; DNA ; Myoviridae ; bacteriophages ; enzymes ; farms ; genes ; genetic databases ; high-throughput nucleotide sequencing ; open reading frames ; pH ; phylogeny ; polymerase chain reaction ; swine ; temperature ; virulence ; wastewater ; China ; covid19
Language	English
Dates of publication	2019-01
Size	p. 33-40.
Publishing place	Springer Vienna
Document type	Article
ZDB-ID	7491-3
ISSN	1432-8798 ; 0304-8608
ISSN (online)	1432-8798
ISSN	0304-8608
DOI	10.1007/s00705-018-4034-0
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Article: Therapeutic Application of Bacteriophage PHB02 and Its Putative Depolymerase Against

Chen, Yibao / Sun, Erchao / Yang, Lan / Song, Jiaoyang / Wu, Bin

Frontiers in microbiology

2018 Volume 9, Page(s) 1678

Abstract: Phage PHB02 specifically ... ...

Abstract	Phage PHB02 specifically infects
Language	English
Publishing date	2018-08-07
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2587354-4
ISSN	1664-302X
ISSN	1664-302X
DOI	10.3389/fmicb.2018.01678
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Article ; Online: Characterisation of a newly detected bacteriophage infecting Bordetella bronchiseptica in swine.

Chen, Yibao / Yang, Lan / Sun, Erchao / Song, Jiaoyang / Wu, Bin

Archives of virology

2018 Volume 164, Issue 1, Page(s) 33–40

Abstract	A novel virulent bacteriophage, vB_BbrM_PHB04, infecting Bordetella bronchiseptica was isolated from wastewater collected at a swine farm in China. Phage vB_BbrM_PHB04 exhibited growth over a wide range of temperature and pH conditions and showed different efficiency of plating values and lytic spectra within the same strains at 25 °C and 37 °C. High-throughput sequencing revealed that vB_BbrM_PHB04 has a linear double-stranded DNA genome with 124 putative open reading frames. Overall, the genome of vB_BbrM_PHB04 showed very low similarity (the highest nucleotide identity 82%, 1% coverage) to other phage sequences in the GenBank database. Phylogenetic analysis indicated that vB_BbrM_PHB04 is a new member of the family Myoviridae. In addition, polymerase chain reaction-based detection of phage genes in phage-resistant B. bronchiseptica variants revealed no evidence of lysogenic activity of phage vB_BbrM_PHB04.
MeSH term(s)	Animals ; Bordetella bronchiseptica/virology ; Genome, Viral ; Hydrogen-Ion Concentration ; Myoviridae/genetics ; Myoviridae/isolation & purification ; Phylogeny ; Swine/microbiology ; Temperature
Keywords	covid19
Language	English
Publishing date	2018-09-18
Publishing country	Austria
Document type	Journal Article
ZDB-ID	7491-3
ISSN	1432-8798 ; 0304-8608
ISSN (online)	1432-8798
ISSN	0304-8608
DOI	10.1007/s00705-018-4034-0
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Article ; Online: Three Salmonella enterica serovar Enteritidis bacteriophages from the Siphoviridae family are promising candidates for phage therapy.

Chen, Yibao / Sun, Erchao / Song, Jiaoyang / Tong, Yigang / Wu, Bin

Canadian journal of microbiology

2018 Volume 64, Issue 11, Page(s) 865–875

Abstract: Salmonella is a common and widely distributed foodborne pathogen that is frequently implicated in gastrointestinal infections. The emergence and spread of Salmonella strains resistant to multiple antibiotics poses a significant health threat, ... ...

Abstract	Salmonella is a common and widely distributed foodborne pathogen that is frequently implicated in gastrointestinal infections. The emergence and spread of Salmonella strains resistant to multiple antibiotics poses a significant health threat, highlighting the urgent need for early and effective therapeutic strategies. We isolated a total of 32 phages from water samples and anal swabs from pigs. Of these, three phages that produced large, clear plaques were selected for further study using the following methods: electron microscopy, analysis of the life cycle parameters, genetic analysis, inhibition of bacterial growth, and activity against biofilms. The three Salmonella phages (vB_SenS_CSP01, vB_SenS_PHB06, and vB_SenS_PHB07) were assigned to the family Siphoviridae on the basis of their morphology. All showed polyvalent infectivity, and individual phages or phage cocktails could inhibit the growth of host Salmonella enterica serovar Enteritidis strains or reduce biofilm formation by Salmonella enterica serovar Typhimurium. In summary, these three phages merit further research as biocontrol agents for Salmonella infection.
MeSH term(s)	Animals ; Biofilms ; Phage Therapy ; Salmonella Infections ; Salmonella Phages/isolation & purification ; Salmonella Phages/physiology ; Salmonella enteritidis/virology ; Serogroup ; Siphoviridae/isolation & purification ; Siphoviridae/physiology ; Swine
Language	English
Publishing date	2018-07-10
Publishing country	Canada
Document type	Journal Article
ZDB-ID	280534-0
ISSN	1480-3275 ; 0008-4166
ISSN (online)	1480-3275
ISSN	0008-4166
DOI	10.1139/cjm-2017-0740
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Article ; Online: Complete Genome Sequence of a Novel T7-Like Bacteriophage from a Pasteurella multocida Capsular Type A Isolate.

Chen, Yibao / Sun, Erchao / Song, Jiaoyang / Yang, Lan / Wu, Bin

Current microbiology

2018 Volume 75, Issue 5, Page(s) 574–579

Abstract: A novel virulent bacteriophage, vB_PmuP_PHB02 (phage PHB02), infecting Pasteurella multocida capsular type A strains, was isolated from wastewater from a swine farm in China. Phage PHB02 has a linear double-stranded DNA genome consisting of 38,670 base ... ...

Abstract	A novel virulent bacteriophage, vB_PmuP_PHB02 (phage PHB02), infecting Pasteurella multocida capsular type A strains, was isolated from wastewater from a swine farm in China. Phage PHB02 has a linear double-stranded DNA genome consisting of 38,670 base pairs (bp), with a G+C content of 40.8% and a 127-bp terminal redundancy. Forty-eight putative open reading frames were identified, and no transfer RNA-encoding genes were detected. The morphology and genomic structure of phage PHB02 resemble those of T7-like phages belonging to the family Podoviridae, of the order Caudovirales. Phage PHB02 was stable over a wide range of temperatures (4-50 °C) and pH values (5.0-9.0), and lysed 30 of the 31 capsular-type-A P. multocida strains tested. Phage PHB02 had no effect on other bacterial species or on P. multocida strains belonging to capsular types D or F.
MeSH term(s)	Animals ; Bacteriophages/classification ; Bacteriophages/genetics ; Bacteriophages/isolation & purification ; Base Composition ; China ; Genome, Viral ; Open Reading Frames ; Pasteurella multocida/virology ; Podoviridae/classification ; Podoviridae/genetics ; Podoviridae/isolation & purification ; Sequence Analysis, DNA ; Sewage/virology ; Swine ; Viral Proteins/genetics
Chemical Substances	Sewage ; Viral Proteins
Language	English
Publishing date	2018-01-06
Publishing country	United States
Document type	Journal Article
ZDB-ID	134238-1
ISSN	1432-0991 ; 0343-8651
ISSN (online)	1432-0991
ISSN	0343-8651
DOI	10.1007/s00284-017-1419-3
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