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Sanchez-Torres V, Kirigo J, Wood TK. Implications of lytic phage infections inducing persistence. Curr Opin Microbiol 2024; 79:102482. [PMID: 38714140 DOI: 10.1016/j.mib.2024.102482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 04/03/2024] [Accepted: 04/15/2024] [Indexed: 05/09/2024]
Abstract
Phage therapy holds much promise as an alternative to antibiotics for fighting infection. However, this approach is no panacea as recent results show that a small fraction of cells survives lytic phage infection due to both dormancy (i.e. formation of persister cells) and resistance (genetic change). In this brief review, we summarize evidence suggesting phages induce the persister state. Therefore, it is predicted that phage cocktails should be combined with antipersister compounds to eradicate bacterial infections.
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Affiliation(s)
- Viviana Sanchez-Torres
- Escuela de Ingeniería Química, Universidad Industrial de Santander, Bucaramanga, Colombia
| | - Joy Kirigo
- Department of Chemical Engineering, Pennsylvania State University, University Park, PA, USA
| | - Thomas K Wood
- Department of Chemical Engineering, Pennsylvania State University, University Park, PA, USA.
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2
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Mukhopadhyay S, Bishayi R, Shaji A, Lee AH, Gupta R, Mohajeri M, Katiyar A, McKee B, Schmitz IR, Shin R, Lele TP, Lele PP. Dynamic Adaptation in Extant Porins Facilitates Antibiotic Tolerance in Energetic Escherichia coli. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.07.583920. [PMID: 38496420 PMCID: PMC10942424 DOI: 10.1101/2024.03.07.583920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Bacteria can tolerate antibiotics despite lacking the genetic components for resistance. The prevailing notion is that tolerance results from depleted cellular energy or cell dormancy. In contrast to this view, many cells in the tolerant population of Escherichia coli can exhibit motility - a phenomenon that requires cellular energy, specifically, the proton-motive force (PMF). As these motile-tolerant cells are challenging to isolate from the heterogeneous tolerant population, their survival mechanism is unknown. Here, we discovered that motile bacteria segregate themselves from the tolerant population under micro-confinement, owing to their unique ability to penetrate micron-sized channels. Single-cell measurements on the motile-tolerant population showed that the cells retained a high PMF, but they did not survive through active efflux alone. By utilizing growth assays, single-cell fluorescence studies, and chemotaxis assays, we showed that the cells survived by dynamically inhibiting the function of existing porins in the outer membrane. A drug transport model for porin-mediated intake and efflux pump-mediated expulsion suggested that energetic tolerant cells withstand antibiotics by constricting their porins. The novel porin adaptation we have uncovered is independent of gene expression changes and may involve electrostatic modifications within individual porins to prevent extracellular ligand entry.
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Fernández-García L, Gao X, Kirigo J, Song S, Battisti ME, Garcia-Contreras R, Tomas M, Guo Y, Wang X, Wood TK. Single-cell analysis reveals that cryptic prophage protease LfgB protects Escherichia coli during oxidative stress by cleaving antitoxin MqsA. Microbiol Spectr 2024; 12:e0347123. [PMID: 38206055 PMCID: PMC10846083 DOI: 10.1128/spectrum.03471-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Accepted: 11/30/2023] [Indexed: 01/12/2024] Open
Abstract
Although toxin/antitoxin (TA) systems are ubiquitous, beyond phage inhibition and mobile element stabilization, their role in host metabolism is obscure. One of the best-characterized TA systems is MqsR/MqsA of Escherichia coli, which has been linked previously to protecting gastrointestinal species during the stress it encounters from the bile salt deoxycholate as it colonizes humans. However, some recent whole-population studies have challenged the role of toxins such as MqsR in bacterial physiology since the mqsRA locus is induced over a hundred-fold during stress, but a phenotype was not found upon its deletion. Here, we investigate further the role of MqsR/MqsA by utilizing single cells and demonstrate that upon oxidative stress, the TA system MqsR/MqsA has a heterogeneous effect on the transcriptome of single cells. Furthermore, we discovered that MqsR activation leads to induction of the poorly characterized yfjXY ypjJ yfjZF operon of cryptic prophage CP4-57. Moreover, deletion of yfjY makes the cells sensitive to H2O2, acid, and heat stress, and this phenotype was complemented. Hence, we recommend yfjY be renamed to lfgB (less fatality gene B). Critically, MqsA represses lfgB by binding the operon promoter, and LfgB is a protease that degrades MqsA to derepress rpoS and facilitate the stress response. Therefore, the MqsR/MqsA TA system facilitates the stress response through cryptic phage protease LfgB.IMPORTANCEThe roles of toxin/antitoxin systems in cell physiology are few and include phage inhibition and stabilization of genetic elements; yet, to date, there are no single-transcriptome studies for toxin/antitoxin systems and few insights for prokaryotes from this novel technique. Therefore, our results with this technique are important since we discover and characterize a cryptic prophage protease that is regulated by the MqsR/MqsA toxin/antitoxin system in order to regulate the host response to oxidative stress.
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Affiliation(s)
- Laura Fernández-García
- Department of Chemical Engineering, Pennsylvania State University, University Park, Pennsylvania, USA
- Microbiology Department, Hospital A Coruña (HUAC), A Coruña, Spain
- Microbiology Translational and Multidisciplinary (MicroTM)‐Research Institute Biomedical A Coruña (INIBIC) and Microbiology, University of A Coruña (UDC), A Coruña, Spain
| | - Xinyu Gao
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Institute of Oceanology, Chinese Academy of Sciences, Nansha, Guangzhou, China
- Guangdong Key Laboratory of Marine Materia Medica, Chinese Academy of Sciences, Nansha, Guangzhou, China
- Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea, Chinese Academy of Sciences, China, Nansha,, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Joy Kirigo
- Department of Chemical Engineering, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Sooyeon Song
- Department of Chemical Engineering, Pennsylvania State University, University Park, Pennsylvania, USA
- Department of Animal Science, Jeonbuk National University, Jeonju-Si, Jellabuk-Do, South Korea
- Department of Agricultural Convergence Technology, Jeonbuk National University, Jeonju-Si, Jellabuk-Do, South Korea
| | - Michael E. Battisti
- Department of Chemical Engineering, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Rodolfo Garcia-Contreras
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico, Mexico
| | - Maria Tomas
- Microbiology Department, Hospital A Coruña (HUAC), A Coruña, Spain
- Microbiology Translational and Multidisciplinary (MicroTM)‐Research Institute Biomedical A Coruña (INIBIC) and Microbiology, University of A Coruña (UDC), A Coruña, Spain
| | - Yunxue Guo
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Institute of Oceanology, Chinese Academy of Sciences, Nansha, Guangzhou, China
- Guangdong Key Laboratory of Marine Materia Medica, Chinese Academy of Sciences, Nansha, Guangzhou, China
- Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea, Chinese Academy of Sciences, China, Nansha,, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Nansha, Guangzhou, China
| | - Xiaoxue Wang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Institute of Oceanology, Chinese Academy of Sciences, Nansha, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Nansha, Guangzhou, China
| | - Thomas K. Wood
- Department of Chemical Engineering, Pennsylvania State University, University Park, Pennsylvania, USA
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Fernández-García L, Song S, Kirigo J, Battisti ME, Petersen ME, Tomás M, Wood TK. Toxin/antitoxin systems induce persistence and work in concert with restriction/modification systems to inhibit phage. Microbiol Spectr 2024; 12:e0338823. [PMID: 38054715 PMCID: PMC10783111 DOI: 10.1128/spectrum.03388-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 11/06/2023] [Indexed: 12/07/2023] Open
Abstract
IMPORTANCE To date, there are no reports of phage infection-inducing persistence. Therefore, our results are important since we show for the first time that a phage-defense system, the MqsRAC toxin/antitoxin system, allows the host to survive infection by forming persister cells, rather than inducing cell suicide. Moreover, we demonstrate that the MqsRAC system works in concert with restriction/modification systems. These results imply that if phage therapy is to be successful, anti-persister compounds need to be administered along with phages.
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Affiliation(s)
- Laura Fernández-García
- Department of Chemical Engineering, Pennsylvania State University, University Park, Pennsylvania, USA
- Microbiology Department of Hospital A Coruña (CHUAC), Microbiology Translational and Multidisciplinary (MicroTM)-Research Institute Biomedical A Coruña (INIBIC) and University of A Coruña (UDC), A Coruña, Spain
| | - Sooyeon Song
- Department of Chemical Engineering, Pennsylvania State University, University Park, Pennsylvania, USA
- Department of Animal Science, Jeonbuk National University, Jeonju-Si, Jellabuk-Do, South Korea
- Agricultural Convergence Technology, Jeonbuk National University, Jeonju-Si, Jellabuk-Do, South Korea
| | - Joy Kirigo
- Department of Chemical Engineering, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Michael E. Battisti
- Department of Chemical Engineering, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Maiken E. Petersen
- Department of Chemical Engineering, Pennsylvania State University, University Park, Pennsylvania, USA
- Interdisciplinary Nanoscience Center, Aarhus University, Aarhus, Denmark
| | - María Tomás
- Microbiology Department of Hospital A Coruña (CHUAC), Microbiology Translational and Multidisciplinary (MicroTM)-Research Institute Biomedical A Coruña (INIBIC) and University of A Coruña (UDC), A Coruña, Spain
| | - Thomas K. Wood
- Department of Chemical Engineering, Pennsylvania State University, University Park, Pennsylvania, USA
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Fernández-García L, Tomás M, Wood TK. Ribosome inactivation by Escherichia coli GTPase RsgA inhibits T4 phage. Front Microbiol 2023; 14:1242163. [PMID: 37670987 PMCID: PMC10475562 DOI: 10.3389/fmicb.2023.1242163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Accepted: 08/07/2023] [Indexed: 09/07/2023] Open
Abstract
Introduction Bacteria must combat phages, and myriad bacterial anti-phage systems have been discovered that reduce host metabolism, for example, by depleting energetic compounds like ATP and NAD+. Hence, these systems indirectly inhibit protein production. Surprisingly, direct reduction of ribosome activity has not been demonstrated to thwart phage. Methods Here, by producing each of the 4,287 Escherichia coli proteins and selecting for anti-phage activity that leads to enhanced growth, we investigated the role of host proteins in phage inhibition. Results and discussion We identified that E. coli GTPase RsgA inhibits lytic phage T4 by inactivating ribosomes.
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Affiliation(s)
- Laura Fernández-García
- Department of Chemical Engineering, Pennsylvania State University, University Park, PA, United States
- Microbiology Translational and Multidisciplinary (MicroTM)-Research Institute Biomedical A Coruña (INIBIC) and Microbiology Department of Hospital A Coruña (CHUAC), University of A Coruña (UDC), A Coruña, Spain
| | - María Tomás
- Microbiology Translational and Multidisciplinary (MicroTM)-Research Institute Biomedical A Coruña (INIBIC) and Microbiology Department of Hospital A Coruña (CHUAC), University of A Coruña (UDC), A Coruña, Spain
| | - Thomas K. Wood
- Department of Chemical Engineering, Pennsylvania State University, University Park, PA, United States
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Zhang Q, Zhou L, Zhao Y, Gao S, Yang Y, Chen Q, Li W, Qi Q, Dong Q, Lei J, Guo X, Gao Q, Yang Y. Uncovering the virome and its interaction with antibiotic resistome during compost fertilization. JOURNAL OF HAZARDOUS MATERIALS 2023; 457:131763. [PMID: 37311294 DOI: 10.1016/j.jhazmat.2023.131763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 05/26/2023] [Accepted: 06/01/2023] [Indexed: 06/15/2023]
Abstract
Antibiotic resistance is a pressing global health issue, leading to increased illnesses and fatalities. The contribution of viruses to the acquisition, preservation, and dissemination of antibiotic resistance genes (ARGs) is not yet fully understood. By using a high-throughput functional gene-based microarray (GeoChip 5.0), this study examines the prevalence and relative abundance of bacteriophage and eukaryotic viral genes in swine manure, compost, compost-amended agricultural soil, and unamended soil from suburban regions of Beijing, China. Our findings reveal a significantly elevated presence of biomarker viral genes in compost-amended soils compared to unamended soils, suggesting potential health risks associated with compost fertilization. We also observed stronger ecological interactions between ARGs and viral genes in manure and compost than in soils. Network analysis identified arabinose efflux permeases and EmrB/QacA resistance genes, linked to CRISPR encoding sequences, as keystone nodes, indicating possible ARG acquisition via virus infections. Moreover, positive correlations were found between viral genes, antibiotic concentrations, and ARG diversity in manure, compost, and compost-amended soils, highlighting a likely pathway for virus-mediated ARG transfer. In summary, our results indicate that use of compost as a fertilizer in agricultural settings could facilitate the spread of ARGs through viral mechanisms, allowing for time-delayed genetic exchanges over broader temporal and spatial scales than ARGs within bacterial genomes.
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Affiliation(s)
- Qingxia Zhang
- Department of Obstetrics and Gynecology, China-Japan Friendship Hospital, Beijing 100029, China
| | - Lei Zhou
- Center for professional training and service, China Association for Science and Technology, China
| | - Yilong Zhao
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Shuhong Gao
- School of Civil and Environmental Engineering, Harbin Institute of Technology (Shenzhen), Shenzhen 518055, China
| | - Yanjun Yang
- Department of Obstetrics and Gynecology, China-Japan Friendship Hospital, Beijing 100029, China
| | - Qingyun Chen
- Department of Obstetrics and Gynecology, China-Japan Friendship Hospital, Beijing 100029, China
| | - Wenhui Li
- Department of Obstetrics and Gynecology, China-Japan Friendship Hospital, Beijing 100029, China
| | - Qi Qi
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Qiang Dong
- Institute of Chemical Defense, Beijing 102205, China
| | - Jiesi Lei
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Xue Guo
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Qun Gao
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China.
| | - Yunfeng Yang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China.
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Nakamura Y, Watanabe K, Yoshioka Y, Ariyoshi W, Yamasaki R. Persister Cell Formation and Elevated lsrA and lsrC Gene Expression upon Hydrogen Peroxide Exposure in a Periodontal Pathogen Aggregatibacter actinomycetemcomitans. Microorganisms 2023; 11:1402. [PMID: 37374903 DOI: 10.3390/microorganisms11061402] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 05/23/2023] [Accepted: 05/25/2023] [Indexed: 06/29/2023] Open
Abstract
The effect of hydrogen peroxide, an antiseptic dental treatment, on Aggregatibacter actinomycetemcomitans, the main causative agent of localized invasive periodontitis, was investigated. Hydrogen peroxide treatment (0.06%, 4× minimum inhibitory concentration) resulted in the persistence and survival of approximately 0.5% of the bacterial population. The surviving bacteria did not genetically acquire hydrogen peroxide resistance but exhibited a known persister behavior. Sterilization with mitomycin C significantly reduced the number of A. actinomycetemcomitans persister survivors. RNA sequencing of hydrogen peroxide-treated A. actinomycetemcomitans showed elevated expression of Lsr family members, suggesting a strong involvement of autoinducer uptake. In this study, we found a risk of A. actinomycetemcomitans persister residual from hydrogen peroxide treatment and hypothesized associated genetic mechanisms of persister from RNA sequencing.
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Affiliation(s)
- Yohei Nakamura
- Division of Infections and Molecular Biology, Department of Health Promotion, Kyushu Dental University, Kitakyushu 803-8580, Fukuoka, Japan
- Division of Developmental Stomatognathic Function Science, Department of Health Promotion, Kyushu Dental University, Kitakyushu 803-8580, Fukuoka, Japan
| | - Koji Watanabe
- Division of Developmental Stomatognathic Function Science, Department of Health Promotion, Kyushu Dental University, Kitakyushu 803-8580, Fukuoka, Japan
| | - Yoshie Yoshioka
- Division of Infections and Molecular Biology, Department of Health Promotion, Kyushu Dental University, Kitakyushu 803-8580, Fukuoka, Japan
| | - Wataru Ariyoshi
- Division of Infections and Molecular Biology, Department of Health Promotion, Kyushu Dental University, Kitakyushu 803-8580, Fukuoka, Japan
| | - Ryota Yamasaki
- Division of Infections and Molecular Biology, Department of Health Promotion, Kyushu Dental University, Kitakyushu 803-8580, Fukuoka, Japan
- Collaborative Research Centre for Green Materials on Environmental Technology, Kyushu Institute of Technology, 1-1 Sensui-chou, Tobata-ku, Kitakyushu 804-8550, Fukuoka, Japan
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Song S, Semenova E, Severinov K, Fernández-García L, Benedik MJ, Maeda T, Wood TK. CRISPR-Cas Controls Cryptic Prophages. Int J Mol Sci 2022; 23:16195. [PMID: 36555835 PMCID: PMC9782134 DOI: 10.3390/ijms232416195] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022] Open
Abstract
The bacterial archetypal adaptive immune system, CRISPR-Cas, is thought to be repressed in the best-studied bacterium, Escherichia coli K-12. We show here that the E. coli CRISPR-Cas system is active and serves to inhibit its nine defective (i.e., cryptic) prophages. Specifically, compared to the wild-type strain, reducing the amounts of specific interfering RNAs (crRNA) decreases growth by 40%, increases cell death by 700%, and prevents persister cell resuscitation. Similar results were obtained by inactivating CRISPR-Cas by deleting the entire 13 spacer region (CRISPR array); hence, CRISPR-Cas serves to inhibit the remaining deleterious effects of these cryptic prophages, most likely through CRISPR array-derived crRNA binding to cryptic prophage mRNA rather than through cleavage of cryptic prophage DNA, i.e., self-targeting. Consistently, four of the 13 E. coli spacers contain complementary regions to the mRNA sequences of seven cryptic prophages, and inactivation of CRISPR-Cas increases the level of mRNA for lysis protein YdfD of cryptic prophage Qin and lysis protein RzoD of cryptic prophage DLP-12. In addition, lysis is clearly seen via transmission electron microscopy when the whole CRISPR-Cas array is deleted, and eliminating spacer #12, which encodes crRNA with complementary regions for DLP-12 (including rzoD), Rac, Qin (including ydfD), and CP4-57 cryptic prophages, also results in growth inhibition and cell lysis. Therefore, we report the novel results that (i) CRISPR-Cas is active in E. coli and (ii) CRISPR-Cas is used to tame cryptic prophages, likely through RNAi, i.e., unlike with active lysogens, active CRISPR-Cas and cryptic prophages may stably co-exist.
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Affiliation(s)
- Sooyeon Song
- Department of Chemical Engineering, Pennsylvania State University, University Park, PA 16802, USA
- Department of Animal Science, Jeonbuk National University, Jeonju-Si 54896, Republic of Korea
- Agricultural Convergence Technology, Jeonbuk National University, Jeonju-Si 54896, Republic of Korea
| | - Ekaterina Semenova
- Waksman Institute of Microbiology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Konstantin Severinov
- Waksman Institute of Microbiology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Laura Fernández-García
- Department of Chemical Engineering, Pennsylvania State University, University Park, PA 16802, USA
| | - Michael J. Benedik
- Office of the Provost, Hamad bin Khalifa University, Education City, Doha P.O. Box 34110, Qatar
| | - Toshinari Maeda
- Department of Biological Functions Engineering, Kyushu Institute of Technology, Kitakyushu 808-0196, Japan
| | - Thomas K. Wood
- Department of Chemical Engineering, Pennsylvania State University, University Park, PA 16802, USA
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