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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 ... ...

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 ; 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, ...

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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Article ; Online: Microbial Communities Associated with Acetaminophen Biodegradation from Mangrove Sediment

Chu-Wen Yang / Yi-En Chen / Bea-Ven Chang

Sustainability, Vol 12, Iss 13, p

2020 Volume 5410

Abstract: Acetaminophen (ACE) is a widely used medicine. Currently, concerns regarding its potential adverse effects on the environments are raised. The aim of this study was to evaluate ACE biodegradation in mangrove sediments under aerobic and anaerobic ... ...

Abstract	Acetaminophen (ACE) is a widely used medicine. Currently, concerns regarding its potential adverse effects on the environments are raised. The aim of this study was to evaluate ACE biodegradation in mangrove sediments under aerobic and anaerobic conditions. Three ACE biodegradation strategies in mangrove sediments were tested. The degradation half-lives ( t 1/2 ) of ACE in the sediments with spent mushroom compost under aerobic conditions ranged from 3.24 ± 0.16 to 6.25 ± 0.31 d. The degradation half-lives ( t 1/2 ) of ACE in sediments with isolated bacterial strains ranged from 2.54 ± 0.13 to 3.30 ± 0.17 d and from 2.62 ± 0.13 to 3.52 ± 0.17 d under aerobic and anaerobic conditions, respectively. The degradation half-lives ( t 1/2 ) of ACE in sediments amended with NaNO 3 , Na 2 SO 4 and NaHCO 3 under anaerobic conditions ranged from 1.16 ± 0.06 to 3.05 ± 0.15 d, 2.39 ± 0.12 to 3.84 ± 0.19 d and 2.79 ± 0.14 to 10.75 ± 0.53 d, respectively. The addition of the three electron acceptors enhanced ACE degradation in mangrove sediments, where NaNO 3 yielded the best effects. Sixteen microbial genera were identified as the major members of microbial communities associated in anaerobic ACE degradation in mangrove sediments with addition of NaNO 3 and Na 2 SO 4 . Three ( Arthrobacter , Enterobacter and Bacillus ) of the sixteen microbial genera were identified in the isolated ACE-degrading bacterial strains.
Keywords	acetaminophen ; mangrove sediments ; biodegradation ; aerobic conditions ; anaerobic conditions ; Environmental effects of industries and plants ; TD194-195 ; Renewable energy sources ; TJ807-830 ; Environmental sciences ; GE1-350
Subject code	550
Language	English
Publishing date	2020-07-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Removal of Organic UV Filters Using Enzymes in Spent Mushroom Composts from Fungicultures

Chu-Wen Yang / Ping-Hsun Tu / Wen-Yi Tso / Bea-Ven Chang

Applied Sciences, Vol 11, Iss 3932, p

2021 Volume 3932

Abstract: Organic UV filters in sunscreen products are released to aquatic ecosystems through human recreational activities and urban wastewater treatment plant effluents. The biodegradation of three organic UV filters, 2-ethylhexyl salicylate (EHS), homosalate ( ... ...

Abstract	Organic UV filters in sunscreen products are released to aquatic ecosystems through human recreational activities and urban wastewater treatment plant effluents. The biodegradation of three organic UV filters, 2-ethylhexyl salicylate (EHS), homosalate (HMS) and ethylhexyl methoxycinnamate (EHMC), which cannot be effectively removed by conventional wastewater treatment plants, was investigated in this study. Spent mushroom compost (SMC), a waste product of the mushroom industry, which contains white-rot fungus extracellular enzymes, was tested for its ability to remove the three organic UV filters. The results of batch experiments revealed that the SMC enzyme extract of Pleurotus djamor exhibited the highest ability for EHS and HMS removal. The results of bioreactor experiments indicated that direct application of SMCs may be a feasible solution to remove EHS and HMS from urban wastewater. The application of SMCs for the removal of organic UV filters can be developed into a green and sustainable technology.
Keywords	sunscreen ; laccases ; wastewater ; mycoremediation ; Technology ; T ; Engineering (General). Civil engineering (General) ; TA1-2040 ; Biology (General) ; QH301-705.5 ; Physics ; QC1-999 ; Chemistry ; QD1-999
Language	English
Publishing date	2021-04-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: A comparative study of short linear motif compositions of the influenza A virus ribonucleoproteins.

Chu-Wen Yang

PLoS ONE, Vol 7, Iss 6, p e

2012 Volume 38637

Abstract: Protein-protein interactions through short linear motifs (SLiMs) are an emerging concept that is different from interactions between globular domains. The SLiMs encode a functional interaction interface in a short (three to ten residues) poorly conserved ...

Abstract	Protein-protein interactions through short linear motifs (SLiMs) are an emerging concept that is different from interactions between globular domains. The SLiMs encode a functional interaction interface in a short (three to ten residues) poorly conserved sequence. This characteristic makes them much more likely to arise/disappear spontaneously via mutations, and they may be more evolutionarily labile than globular domains. The diversity of SLiM composition may provide functional diversity for a viral protein from different viral strains. This study is designed to determine the different SLiM compositions of ribonucleoproteins (RNPs) from influenza A viruses (IAVs) from different hosts and with different levels of virulence. The 96 consensus sequences (regular expressions) of SLiMs from the ELM server were used to conduct a comprehensive analysis of the 52,513 IAV RNP sequences. The SLiM compositions of RNPs from IAVs from different hosts and with different levels of virulence were compared. The SLiM compositions of 845 RNPs from highly virulent/pandemic IAVs were also analyzed. In total, 292 highly conserved SLiMs were found in RNPs regardless of the IAV host range. These SLiMs may be basic motifs that are essential for the normal functions of RNPs. Moreover, several SLiMs that are rare in seasonal IAV RNPs but are present in RNPs from highly virulent/pandemic IAVs were identified.The SLiMs identified in this study provide a useful resource for experimental virologists to study the interactions between IAV RNPs and host intracellular proteins. Moreover, the SLiM compositions of IAV RNPs also provide insights into signal transduction pathways and protein interaction networks with which IAV RNPs might be involved. Information about SLiMs might be useful for the development of anti-IAV drugs.
Keywords	Medicine ; R ; Science ; Q
Subject code	570
Language	English
Publishing date	2012-01-01T00:00:00Z
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: Uncovering the Potential Pan Proteomes Encoded by Genomic Strand RNAs of Influenza A Viruses.

Chu-Wen Yang / Mei-Fang Chen

PLoS ONE, Vol 11, Iss 1, p e

2016 Volume 0146936

Abstract: Influenza A virus genomes are composed of eight negative sense RNAs. In total, 16 proteins encoded by eight positive sense RNAs were identified. One putative protein coding sequence (PCS) encoded by genomic strand RNA of segment 8 has been previously ... ...

Abstract	Influenza A virus genomes are composed of eight negative sense RNAs. In total, 16 proteins encoded by eight positive sense RNAs were identified. One putative protein coding sequence (PCS) encoded by genomic strand RNA of segment 8 has been previously proposed. In this study, 95,608, 123,965 and 35,699 genomic strand RNA sequences from influenza A viruses from avian, human and mammalian hosts, respectively, were used to identify PCSs encoded by the genomic strand RNAs. In total, 326,069 PCSs with lengths equal to or longer than 80 amino acids were identified and clustered into 270 PCS groups. Twenty of the 270 PCS groups which have greater than 10% proportion in influenza A viruses from avian, human or mammalian hosts were selected for detailed study. Maps of the 20 PCSGs in the influenza A virus genomes were constructed. The proportions of the 20 PCSGs in influenza A viruses from different hosts and serotypes were analyzed. One secretory and five membrane proteins predicted from the PCS groups encoded by genomic strand RNAs of segments 1, 2, 4, 6, 7 and 8 were identified. These results suggest the possibility of the ambisense nature of the influenza A virus genomic RNAs and a potential coding sequence reservoir encoding potential pan proteomes of influenza A viruses.
Keywords	Medicine ; R ; Science ; Q
Subject code	500 ; 572
Language	English
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: Biodegradation of Malachite Green in Milkfish Pond Sediments

Chu-Wen Yang / Wei-Liang Chao / Chi-Yen Hsieh / Bea-Ven Chang

Sustainability, Vol 11, Iss 15, p

2019 Volume 4179

Abstract: Malachite green (MG) is usually applied as a biocide in aquaculture worldwide. The microbial degradation of MG and changes in the microbial community composition of milkfish ( Chanos chanos ) culture pond sediments were assessed in this study. Three MG- ... ...

Abstract	Malachite green (MG) is usually applied as a biocide in aquaculture worldwide. The microbial degradation of MG and changes in the microbial community composition of milkfish ( Chanos chanos ) culture pond sediments were assessed in this study. Three MG-degrading bacteria strains—M6, M10, and M12—were isolated, identified, and characterized. Strains M6, M10, and M12 are closely related to Zhouia amylolytica, Tenacibaculum mesophilum , and Enterobacter cloacae, respectively. The bacterial strains M10 and M12 showed good ability to degrade MG in the sediment. The MG degradation rate was increased after adding MG three more times. The microbial community in the sediment changes with different treatments. The bacterial strains M10 and M12 provide a potential solution for the treatment of sediment of saline aquaculture ponds with MG contamination.
Keywords	malachite green ; milkfish pond sediment ; biodegradation ; Environmental effects of industries and plants ; TD194-195 ; Renewable energy sources ; TJ807-830 ; Environmental sciences ; GE1-350
Subject code	550
Language	English
Publishing date	2019-08-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: A Novel Phytogenic Formulation, EUBIO-BPSG, as a Promising One Health Approach to Replace Antibiotics and Promote Reproduction Performance in Laying Hens

Hieu Tran Nguyen Minh / Tien-Fen Kuo / Wen-Yu Lin / Tzu-Chia Peng / Greta Yang / Chih-Yu Lin / Ting-Hsiang Chang / Yu-Liang Yang / Cheng-Hsun Ho / Bor-Rung Ou / Chu-Wen Yang / Yu-Chuan Liang / Wen-Chin Yang

Bioengineering, Vol 10, Iss 346, p

2023 Volume 346

Abstract: Gut microbiota play a key role in health maintenance and disease pathogenesis in animals. Dietary phytochemicals are crucial factors shaping gut bacteria. Here, we investigated the function and mechanism of a phytogenic formulation, EUBIO-BPSG (BP), in ... ...

Abstract	Gut microbiota play a key role in health maintenance and disease pathogenesis in animals. Dietary phytochemicals are crucial factors shaping gut bacteria. Here, we investigated the function and mechanism of a phytogenic formulation, EUBIO-BPSG (BP), in laying hens. We found that BP dose-dependently improved health and egg production in 54-week-old hens. Furthermore, BP was correlated with increased fecal Lactobacillus , decreased Escherichia coli and Salmonella enterica , and reduced antibiotic resistance (AR) and antibiotic resistance genes (ARG) in chicken stools. The 16S rDNA data showed that BP increased seven genera of probiotics and reduced 13 genera of pathogens in chicken feces. In vitro co-culture experiments showed that BP at 4 µg/mL and above promoted growth of L. reuteri while large 100- and 200-fold higher doses suppressed growth of E. coli and S. enterica , respectively. Mechanistic studies indicated that L. reuteri and its supernatants antagonized growth of E. coli and S. enterica but not vice-versa. Five short-chain fatty acids and derivatives (SCFA) produced from L. reuteri directly killed both pathogens via membrane destruction. Furthermore, BP inhibited conjugation and recombination of ARG via interference with conjugation machinery and integrase activity in E. coli . Collectively, this work suggests that BP promotes host health and reproductive performance in laying hens through regulation of gut microbiota through increasing probiotics and decreasing pathogens and spreading ARG.
Keywords	antibiotic resistance genes (ARG) ; antibiotic resistance (AR) ; EUBIO-BPSG ; gut microbiota ; laying hens ; short-chain fatty acids and derivatives (SCFA) ; Technology ; T ; Biology (General) ; QH301-705.5
Language	English
Publishing date	2023-03-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Curcumin Induces p53-Null Hepatoma Cell Line Hep3B Apoptosis through the AKT-PTEN-FOXO4 Pathway

An-Ting Liou / Mei-Fang Chen / Chu-Wen Yang

Evidence-Based Complementary and Alternative Medicine, Vol

2017 Volume 2017

Abstract: Objective. Curcumin (diferuloylmethane) is a yellow-colored polyphenol with antiproliferative and proapoptotic activities to various types of cancer cells. This study explored the mechanism by which curcumin induces p53-null hepatoma cell apoptosis. ... ...

Abstract	Objective. Curcumin (diferuloylmethane) is a yellow-colored polyphenol with antiproliferative and proapoptotic activities to various types of cancer cells. This study explored the mechanism by which curcumin induces p53-null hepatoma cell apoptosis. Results. AKT, FOXO1, and FOXO3 proteins were downregulated after curcumin treatment. Conversely, PTEN was upregulated. Subcellular fractionations revealed that the FOXO4 protein translocated from cytosol into the nucleus after curcumin treatment. Overexpression of FOXO4 increases the sensitivity of Hep3B cells to curcumin. Knockdown of the FOXO4 gene by siRNA inhibits the proapoptotic effects of curcumin on Hep3B cell. Conclusions. This study revealed the AKT/PTEN/FOXO4 pathway as a potential candidate of target for treatment of p53-null liver cancers.
Keywords	Other systems of medicine ; RZ201-999
Language	English
Publishing date	2017-01-01T00:00:00Z
Publisher	Hindawi Limited
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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