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Book: Chu wen hua

Yang, Quanxi

(20 shi ji zhong guo wen wu kao gu fa xian yu yan jiu cong shu ; 20世纪中国文物考古发现与研究丛书)

2003

Author's details	Yang quan xi
Series title	20 shi ji zhong guo wen wu kao gu fa xian yu yan jiu cong shu ; 20世纪中国文物考古发现与研究丛书
Language	Chinese
Dates of publication	2003-2000
Size	245 p, Ill
Edition	Di 1 ban, di 2 ci yin shua
Publisher	Wen wu chu ban she
Publishing place	Bei jing
Document type	Book
ISBN	7501012164 ; 9787501012169
Database	Former special subject collection: coastal and deep sea fishing

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Article ; Online: Parabens Increase Sulfamethoxazole-, Tetracycline- and Paraben-Resistant Bacteria and Reshape the Nitrogen/Sulfur Cycle-Associated Microbial Communities in Freshwater River Sediments.

Yang, Chu-Wen / Lee, Wei-Chen

Toxics

2023 Volume 11, Issue 4

Abstract: ... ...

Abstract	Backgrounds
Language	English
Publishing date	2023-04-18
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2733883-6
ISSN	2305-6304 ; 2305-6304
ISSN (online)	2305-6304
ISSN	2305-6304
DOI	10.3390/toxics11040387
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Low compositions of human toll-like receptor 7/8-stimulating RNA motifs in the MERS-CoV, SARS-CoV and SARS-CoV-2 genomes imply a substantial ability to evade human innate immunity.

Yang, Chu-Wen / Chen, Mei-Fang

PeerJ

2021 Volume 9, Page(s) e11008

Abstract: Background: The innate immune system especially Toll-like receptor (TLR) 7/8 and the interferon pathway, constitutes an important first line of defense against single-stranded RNA viruses. However, large-scale, systematic comparisons of the TLR 7/8- ... ...

Abstract	Background: The innate immune system especially Toll-like receptor (TLR) 7/8 and the interferon pathway, constitutes an important first line of defense against single-stranded RNA viruses. However, large-scale, systematic comparisons of the TLR 7/8-stimulating potential of genomic RNAs of single-stranded RNA viruses are rare. In this study, a computational method to evaluate the human TLR 7/8-stimulating ability of single-stranded RNA virus genomes based on their human TLR 7/8-stimulating trimer compositions was used to analyze 1,002 human coronavirus genomes. Results: The human TLR 7/8-stimulating potential of coronavirus genomic (positive strand) RNAs followed the order of NL63-CoV > HKU1-CoV >229E-CoV ≅ OC63-CoV > SARS-CoV-2 > MERS-CoV > SARS-CoV. These results suggest that among these coronaviruses, MERS-CoV, SARS-CoV and SARS-CoV-2 may have a higher ability to evade the human TLR 7/8-mediated innate immune response. Analysis with a logistic regression equation derived from human coronavirus data revealed that most of the 1,762 coronavirus genomic (positive strand) RNAs isolated from bats, camels, cats, civets, dogs and birds exhibited weak human TLR 7/8-stimulating potential equivalent to that of the MERS-CoV, SARS-CoV and SARS-CoV-2 genomic RNAs. Conclusions: Prediction of the human TLR 7/8-stimulating potential of viral genomic RNAs may be useful for surveillance of emerging coronaviruses from nonhuman mammalian hosts.
Language	English
Publishing date	2021-02-24
Publishing country	United States
Document type	Journal Article
ZDB-ID	2703241-3
ISSN	2167-8359
ISSN	2167-8359
DOI	10.7717/peerj.11008
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Uncovering potential host proteins and pathways that may interact with eukaryotic short linear motifs in viral proteins of MERS, SARS and SARS2 coronaviruses that infect humans.

Yang, Chu-Wen / Shi, Zhi-Ling

PloS one

2021 Volume 16, Issue 2, Page(s) e0246150

Abstract: A coronavirus pandemic caused by a novel coronavirus (SARS-CoV-2) has spread rapidly worldwide since December 2019. Improved understanding and new strategies to cope with novel coronaviruses are urgently needed. Viruses (especially RNA viruses) encode a ... ...

Abstract	A coronavirus pandemic caused by a novel coronavirus (SARS-CoV-2) has spread rapidly worldwide since December 2019. Improved understanding and new strategies to cope with novel coronaviruses are urgently needed. Viruses (especially RNA viruses) encode a limited number and size (length of polypeptide chain) of viral proteins and must interact with the host cell components to control (hijack) the host cell machinery. To achieve this goal, the extensive mimicry of SLiMs in host proteins provides an effective strategy. However, little is known regarding SLiMs in coronavirus proteins and their potential targets in host cells. The objective of this study is to uncover SLiMs in coronavirus proteins that are present within host cells. These SLiMs have a high possibility of interacting with host intracellular proteins and hijacking the host cell machinery for virus replication and dissemination. In total, 1,479 SLiM hits were identified in the 16 proteins of 590 coronaviruses infecting humans. Overall, 106 host proteins were identified that may interact with SLiMs in 16 coronavirus proteins. These SLiM-interacting proteins are composed of many intracellular key regulators, such as receptors, transcription factors and kinases, and may have important contributions to virus replication, immune evasion and viral pathogenesis. A total of 209 pathways containing proteins that may interact with SLiMs in coronavirus proteins were identified. This study uncovers potential mechanisms by which coronaviruses hijack the host cell machinery. These results provide potential therapeutic targets for viral infections.
Language	English
Publishing date	2021-02-03
Publishing country	United States
Document type	Journal Article
ISSN	1932-6203
ISSN (online)	1932-6203
DOI	10.1371/journal.pone.0246150
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: The Effects of Preservatives on Antibiotic- and Preservative-Resistant Microbes and Nitrogen/Sulfur Cycle Associated Microbial Communities in Freshwater River Sediments.

Liao, Chien-Sen / Cao, Xuan-Di / Lee, Wei-Chen / Yang, Chu-Wen

Antibiotics (Basel, Switzerland)

2023 Volume 12, Issue 7

Abstract: The intensive use of benzoic acid (BA), 4-hydroxybenzoic acid (HB), and dehydroacetate (DHA) as additives and preservatives in cosmetics and foods causes emerging environmental pollutions. Anthropogenic releases of BA, HB and DHA are primarily emissions ... ...

Abstract	The intensive use of benzoic acid (BA), 4-hydroxybenzoic acid (HB), and dehydroacetate (DHA) as additives and preservatives in cosmetics and foods causes emerging environmental pollutions. Anthropogenic releases of BA, HB and DHA are primarily emissions into water and soil. However, few studies investigate the effects of BA, HB and DHA on microbial communities in freshwater river sediments. The aim of this study is to reveal the effects of BA, HB and DHA on microbial communities in freshwater river sediments. Tetracycline-, sulfamethoxazole- and preservative-resistant microbes were increased in the river sediments treated with BA, HB and DHA. The relative abundances of methanogen- and xenobiotic-degradation-associated microbial communities were also increased in the BA-, HB- and DHA-treated sediments. The relative abundance of four nitrogen cycle associated microbial groups (anammox, nitrogen fixation, denitrification, and dissimilatory nitrate reduction) were increased after the eighth week in the BA-, HB- and DHA-treated sediments. For the sulfur cycle, the relative abundance of thiosulfate oxidation associated microbial communities were increased after the eighth week in the BA-, HB- and DHA-treated sediments. Results of this study provide insight into the effects of BA, HB and DHA on antibiotic resistance, nitrogen cycle, sulfur cycle, drug resistance and methane production in freshwater aquatic environments.
Language	English
Publishing date	2023-06-21
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2681345-2
ISSN	2079-6382
ISSN	2079-6382
DOI	10.3390/antibiotics12071082
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Composition of human-specific slow codons and slow di-codons in SARS-CoV and 2019-nCoV are lower than other coronaviruses suggesting a faster protein synthesis rate of SARS-CoV and 2019-nCoV.

Yang, Chu-Wen / Chen, Mei-Fang

Journal of microbiology, immunology, and infection = Wei mian yu gan ran za zhi

2020 Volume 53, Issue 3, Page(s) 419–424

Abstract: Translation of a genetic codon without a cognate tRNA gene is affected by both the cognate tRNA availability and the interaction with non-cognate isoacceptor tRNAs. Moreover, two consecutive slow codons (slow di-codons) lead to a much slower translation ... ...

Abstract	Translation of a genetic codon without a cognate tRNA gene is affected by both the cognate tRNA availability and the interaction with non-cognate isoacceptor tRNAs. Moreover, two consecutive slow codons (slow di-codons) lead to a much slower translation rate. Calculating the composition of host specific slow codons and slow di-codons in the viral protein coding sequences can predict the order of viral protein synthesis rates between different virus strains. Comparison of human-specific slow codon and slow di-codon compositions in the genomes of 590 coronaviruses infect humans revealed that the protein synthetic rates of 2019 novel coronavirus (2019-nCoV) and severe acute respiratory syndrome-related coronavirus (SARS-CoV) may be much faster than other coronaviruses infect humans. Analysis of host-specific slow codon and di-codon compositions provides links between viral genomic sequences and capability of virus replication in host cells that may be useful for surveillance of the transmission potential of novel viruses.
MeSH term(s)	Betacoronavirus/genetics ; Codon/genetics ; Genome, Viral/genetics ; Humans ; Phylogeny ; Protein Biosynthesis/genetics ; RNA, Transfer/genetics ; SARS Virus/genetics ; SARS-CoV-2 ; Virus Replication/physiology
Chemical Substances	Codon ; RNA, Transfer (9014-25-9)
Keywords	covid19
Language	English
Publishing date	2020-03-10
Publishing country	England
Document type	Journal Article
ZDB-ID	1497590-7
ISSN	1995-9133 ; 1684-1182 ; 0253-2662
ISSN (online)	1995-9133
ISSN	1684-1182 ; 0253-2662
DOI	10.1016/j.jmii.2020.03.002
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Uncovering potential host proteins and pathways that may interact with eukaryotic short linear motifs in viral proteins of MERS, SARS and SARS2 coronaviruses that infect humans.

Chu-Wen Yang / Zhi-Ling Shi

PLoS ONE, Vol 16, Iss 2, p e

2021 Volume 0246150

Abstract	A coronavirus pandemic caused by a novel coronavirus (SARS-CoV-2) has spread rapidly worldwide since December 2019. Improved understanding and new strategies to cope with novel coronaviruses are urgently needed. Viruses (especially RNA viruses) encode a limited number and size (length of polypeptide chain) of viral proteins and must interact with the host cell components to control (hijack) the host cell machinery. To achieve this goal, the extensive mimicry of SLiMs in host proteins provides an effective strategy. However, little is known regarding SLiMs in coronavirus proteins and their potential targets in host cells. The objective of this study is to uncover SLiMs in coronavirus proteins that are present within host cells. These SLiMs have a high possibility of interacting with host intracellular proteins and hijacking the host cell machinery for virus replication and dissemination. In total, 1,479 SLiM hits were identified in the 16 proteins of 590 coronaviruses infecting humans. Overall, 106 host proteins were identified that may interact with SLiMs in 16 coronavirus proteins. These SLiM-interacting proteins are composed of many intracellular key regulators, such as receptors, transcription factors and kinases, and may have important contributions to virus replication, immune evasion and viral pathogenesis. A total of 209 pathways containing proteins that may interact with SLiMs in coronavirus proteins were identified. This study uncovers potential mechanisms by which coronaviruses hijack the host cell machinery. These results provide potential therapeutic targets for viral infections.
Keywords	Medicine ; R ; Science ; Q
Subject code	572 ; 570
Language	English
Publishing date	2021-01-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Low compositions of human toll-like receptor 7/8-stimulating RNA motifs in the MERS-CoV, SARS-CoV and SARS-CoV-2 genomes imply a substantial ability to evade human innate immunity

Chu-Wen Yang / Mei-Fang Chen

PeerJ, Vol 9, p e

2021 Volume 11008

Abstract: Background The innate immune system especially Toll-like receptor (TLR) 7/8 and the interferon pathway, constitutes an important first line of defense against single-stranded RNA viruses. However, large-scale, systematic comparisons of the TLR 7/8- ... ...

Abstract	Background The innate immune system especially Toll-like receptor (TLR) 7/8 and the interferon pathway, constitutes an important first line of defense against single-stranded RNA viruses. However, large-scale, systematic comparisons of the TLR 7/8-stimulating potential of genomic RNAs of single-stranded RNA viruses are rare. In this study, a computational method to evaluate the human TLR 7/8-stimulating ability of single-stranded RNA virus genomes based on their human TLR 7/8-stimulating trimer compositions was used to analyze 1,002 human coronavirus genomes. Results The human TLR 7/8-stimulating potential of coronavirus genomic (positive strand) RNAs followed the order of NL63-CoV > HKU1-CoV >229E-CoV ≅ OC63-CoV > SARS-CoV-2 > MERS-CoV > SARS-CoV. These results suggest that among these coronaviruses, MERS-CoV, SARS-CoV and SARS-CoV-2 may have a higher ability to evade the human TLR 7/8-mediated innate immune response. Analysis with a logistic regression equation derived from human coronavirus data revealed that most of the 1,762 coronavirus genomic (positive strand) RNAs isolated from bats, camels, cats, civets, dogs and birds exhibited weak human TLR 7/8-stimulating potential equivalent to that of the MERS-CoV, SARS-CoV and SARS-CoV-2 genomic RNAs. Conclusions Prediction of the human TLR 7/8-stimulating potential of viral genomic RNAs may be useful for surveillance of emerging coronaviruses from nonhuman mammalian hosts.
Keywords	Toll-like receptor 7/8 ; Immunostimulating RNA motifs ; SARS-CoV-2 ; Medicine ; R ; Biology (General) ; QH301-705.5
Subject code	572
Language	English
Publishing date	2021-02-01T00:00:00Z
Publisher	PeerJ Inc.
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Application of Fungus Enzymes in Spent Mushroom Composts from Edible Mushroom Cultivation for Phthalate Removal.

Chang, Bea-Ven / Yang, Chiao-Po / Yang, Chu-Wen

Microorganisms

2021 Volume 9, Issue 9

Abstract: Spent mushroom composts (SMCs) are waste products of mushroom cultivation. The handling of large amounts of SMCs has become an important environmental issue. Phthalates are plasticizers which are widely distributed in the environment and urban wastewater, ...

Abstract	Spent mushroom composts (SMCs) are waste products of mushroom cultivation. The handling of large amounts of SMCs has become an important environmental issue. Phthalates are plasticizers which are widely distributed in the environment and urban wastewater, and cannot be effectively removed by conventional wastewater treatment methods. In this study, SMCs are tested for their ability to remove phthalates, including benzyl butyl phthalate (BBP), di-n-butyl phthalate (DBP), and diethyl phthalate (DEP). Batch experiments reveal that BBP, DBP, and DEP can be degraded by the SMC enzyme extracts of four edible mushrooms:
Language	English
Publishing date	2021-09-19
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2720891-6
ISSN	2076-2607
ISSN	2076-2607
DOI	10.3390/microorganisms9091989
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Application of Fungus Enzymes in Spent Mushroom Composts from Edible Mushroom Cultivation for Phthalate Removal

Bea-Ven Chang / Chiao-Po Yang / Chu-Wen Yang

Microorganisms, Vol 9, Iss 1989, p

2021 Volume 1989

Abstract	Spent mushroom composts (SMCs) are waste products of mushroom cultivation. The handling of large amounts of SMCs has become an important environmental issue. Phthalates are plasticizers which are widely distributed in the environment and urban wastewater, and cannot be effectively removed by conventional wastewater treatment methods. In this study, SMCs are tested for their ability to remove phthalates, including benzyl butyl phthalate (BBP), di-n-butyl phthalate (DBP), and diethyl phthalate (DEP). Batch experiments reveal that BBP, DBP, and DEP can be degraded by the SMC enzyme extracts of four edible mushrooms: Pleurotus eryngii , Pleurotus djamor , Pleurotus ostreatus , and Auricularia polytricha . Potential fungus enzymes associated with BBP, DBP, and DEP degradation in SMCs (i.e., esterases, oxygenases, and oxidases/dehydrogenases) are uncovered by metaproteomic analysis using mass spectrometry. Bioreactor experiments indicate that the direct application of SMCs can remove BBP, DBP, and DEP from wastewater, through adsorption and biodegradation. The results of this study extend the application of white-rot fungi without laccases (e.g., Auricularia sp.) for the removal of organic pollutants which are not degraded by laccases. The application of SMCs for phthalate removal can be developed into a mycoremediation-based green and sustainable technology.
Keywords	fungus enzymes ; mycoremediation ; phthalates ; Biology (General) ; QH301-705.5
Subject code	660
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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