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Chen G, Shi H, Ding H, Zhang X, Gu T, Zhu M, Tan W. Multi-scale analysis of nickel ion tolerance mechanism for thermophilic Sulfobacillus thermosulfidooxidans in bioleaching. JOURNAL OF HAZARDOUS MATERIALS 2023; 443:130245. [PMID: 36332278 DOI: 10.1016/j.jhazmat.2022.130245] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 10/11/2022] [Accepted: 10/20/2022] [Indexed: 06/16/2023]
Abstract
Bioleaching is intensively investigated for recovering valuable metals such as Li, Co, Ni and Cu. Nickel ion stress threatens the health of microorganisms when Ni2+ starts to accumulate in the leachate during the bioleaching of materials that are rich in Ni, such as spent lithium-ion batteries. The possible mechanisms underlying the response of S. thermosulfidooxidans to nickel ion stress were analyzed using a multi-scale approach. Under the condition of nickel ion stress, high concentrations of nickel ions were immobilized by extracellular polymeric substances, while concentrations of nickel ions inside the cells remained low. The intracellular adenosine triphosphate (ATP) concentration and H+-ATPase activity increased to maintain normal cell growth and metabolic activities. Scavenging abilities of S. thermosulfidooxidans for hydrogen peroxide and superoxide anion were enhanced to reduce oxidative damage induced by nickel ion stress. There were 734 differentially expressed genes identified by RNA-seq under nickel ion stress. Most of them were involved in oxidative phosphorylation, glutathione metabolism and genetic information processing, responsible for intracellular energy utilization, intracellular antioxidant capacity and DNA damage repair, respectively. The results of this study are of major significance for in-depth understanding of the mechanisms of acidophilic microorganisms' resistance to metal ions.
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Affiliation(s)
- Guanglin Chen
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Hongjie Shi
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Huili Ding
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Xu Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China.
| | - Tingyue Gu
- Department of Chemical and Biomolecular Engineering, Institute for Sustainable Energy and the Environment, Ohio University, Athens, OH, United States
| | - Minglong Zhu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Wensong Tan
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
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Autoimmune Effect of Antibodies against the SARS-CoV-2 Nucleoprotein. Viruses 2022; 14:v14061141. [PMID: 35746613 PMCID: PMC9228376 DOI: 10.3390/v14061141] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 05/20/2022] [Accepted: 05/23/2022] [Indexed: 01/27/2023] Open
Abstract
COVID-19 caused by SARS-CoV-2 is continuing to spread around the world and drastically affect our daily life. New strains appear, and the severity of the course of the disease itself seems to be decreasing, but even people who have been ill on an outpatient basis suffer post-COVID consequences. Partly, it is associated with the autoimmune reactions, so debates about the development of new vaccines and the need for vaccination/revaccination continue. In this study we performed an analysis of the antibody response of patients with COVID-19 to linear and conformational epitopes of viral proteins using ELISA, chip array and western blot with analysis of correlations between antibody titer, disease severity, and complications. We have shown that the presence of IgG antibodies to the nucleoprotein can deteriorate the course of the disease, induce multiple direct COVID-19 symptoms, and contribute to long-term post-covid symptoms. We analyzed the cross reactivity of antibodies to SARS-CoV-2 with own human proteins and showed that antibodies to the nucleocapsid protein can bind to human proteins. In accordance with the possibility of HLA presentation, the main possible targets of the autoantibodies were identified. People with HLA alleles A01:01; A26:01; B39:01; B15:01 are most susceptible to the development of autoimmune processes after COVID-19.
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Proteomic Analysis of the Antibacterial Effect of Improved Dian Dao San against Propionibacterium acnes. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2022; 2022:3855702. [PMID: 35186097 PMCID: PMC8849895 DOI: 10.1155/2022/3855702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Revised: 01/09/2022] [Accepted: 01/13/2022] [Indexed: 12/01/2022]
Abstract
Propionibacterium acnes (P. acnes) is a major pathogen of acne vulgaris. The traditional Chinese medicine (TCM) compound prescription, Dian Dao San (DDS), is effective for treating P. acnes. Previous clinical work by our team demonstrated that improved Dian Dao San (IDDS) has better antibacterial effects. However, the mechanism of IDDS inhibition of P. acnes is still unknown. Hence, the isobaric tags for relative and absolute quantitation (iTRAQ) technology was applied to explore the antibacterial mechanism of IDDS against P. acnes. Our results suggested that the antibacterial mechanism of IDDS was related to the glycolytic pathway. gap, pgk, and tpiA enzymes were found to be potential target proteins in the bacterial glycolytic pathway as an antibacterial mechanism of inhibition. In addition, SEM and TEM analyses revealed that IDDS may destruct bacterial plasma membrane and cell wall. The results provide a reliable, direct, and scientific theoretical basis for wide application of IDDS.
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Chen SY, Wu JQ, Sung S. Effects of sulfur dosage on continuous bioleaching of heavy metals from contaminated sediment. JOURNAL OF HAZARDOUS MATERIALS 2022; 424:127257. [PMID: 34601403 DOI: 10.1016/j.jhazmat.2021.127257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 09/07/2021] [Accepted: 09/14/2021] [Indexed: 06/13/2023]
Abstract
The bioleaching technology has been considered as a promising green technology for remediation of contaminated sediments in recent years. Bioleaching technology was generally conducted in the batch bioreactor; however, the continuous bioreactor should be developed for the application of bioleaching technology in the future. The purposes of this study were to establish a continuous bioleaching process, and to evaluate the effects of sulfur dosage on the efficiency of metal removal during this continuous bioleaching process. The obtained results show that the pH decrease, sulfate production and metal removal efficiency all increased with increasing sulfur dosage in the continuous bioleaching process due to high substrate concentration for sulfur-oxidizing bacteria. After 30 days of operation time, the maximum solubilization efficiencies for Zn, Ni, Cu and Cr were found to be 78%, 90%, 88% and 68%, respectively, at 5% of sulfur dosage. After the bioleaching process, heavy metals bound in the carbonates, Fe-Mn oxides and organics/sulfides in the sediment were effectively removed and the potential ecological and toxic risks of treated sediment were greatly reduced. The results of bacterial community analyses demonstrated that this continuous bioleaching process were dominated by several acidophilic sulfur-oxidizing bacteria; S. thermosulfidooxidans, At. thiooxidans/At. ferrooxidans, S. thermotolerans and At. albertensis, whereas the percentage of less-acidophilic sulfur-oxidizing bacteria (T. thioparus and T. cuprina) was lower than 15% of total bacteria. In addition, the cell numbers of sulfur-oxidizing bacteria increased as the sulfur dosage was increased in the continuous bioleaching process.
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Affiliation(s)
- Shen-Yi Chen
- Department of Safety, Health and Environmental Engineering, National Kaohsiung University of Science and Technology, Kaohsiung 811, Taiwan, ROC.
| | - Jun-Qi Wu
- Department of Safety, Health and Environmental Engineering, National Kaohsiung University of Science and Technology, Kaohsiung 811, Taiwan, ROC
| | - Shihwu Sung
- College of Agriculture, Forestry and Natural Resource Management, University of Hawaii at Hilo, Hilo, HI 96720-4091, USA
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Trongtrakul K, Thonusin C, Pothirat C, Chattipakorn SC, Chattipakorn N. Past Experiences for Future Applications of Metabolomics in Critically Ill Patients with Sepsis and Septic Shocks. Metabolites 2021; 12:metabo12010001. [PMID: 35050123 PMCID: PMC8779293 DOI: 10.3390/metabo12010001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 12/16/2021] [Accepted: 12/18/2021] [Indexed: 12/17/2022] Open
Abstract
A disruption of several metabolic pathways in critically ill patients with sepsis indicates that metabolomics might be used as a more precise tool for sepsis and septic shock when compared with the conventional biomarkers. This article provides information regarding metabolomics studies in sepsis and septic shock patients. It has been shown that a variety of metabolomic pathways are altered in sepsis and septic shock, including amino acid metabolism, fatty acid oxidation, phospholipid metabolism, glycolysis, and tricarboxylic acid cycle. Based upon this comprehensive review, here, we demonstrate that metabolomics is about to change the world of sepsis biomarkers, not only for its utilization in sepsis diagnosis, but also for prognosticating and monitoring the therapeutic response. Additionally, the future direction regarding the establishment of studies integrating metabolomics with other molecular modalities and studies identifying the relationships between metabolomic profiles and clinical characteristics to address clinical application are discussed in this article. All of the information from this review indicates the important impact of metabolomics as a tool for diagnosis, monitoring therapeutic response, and prognostic assessment of sepsis and septic shock. These findings also encourage further clinical investigations to warrant its use in routine clinical settings.
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Affiliation(s)
- Konlawij Trongtrakul
- Department of Internal Medicine, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand; (K.T.); (C.P.)
| | - Chanisa Thonusin
- Metabolomics Unit, Cardiac Electrophysiology Research and Training Center, Chiang Mai University, Chiang Mai 50200, Thailand;
- Center of Excellence in Cardiac Electrophysiology Research, Chiang Mai University, Chiang Mai 50200, Thailand
- Cardiac Electrophysiology Unit, Department of Physiology, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand
- Correspondence: (C.T.); (N.C.)
| | - Chaicharn Pothirat
- Department of Internal Medicine, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand; (K.T.); (C.P.)
| | - Siriporn C. Chattipakorn
- Metabolomics Unit, Cardiac Electrophysiology Research and Training Center, Chiang Mai University, Chiang Mai 50200, Thailand;
- Center of Excellence in Cardiac Electrophysiology Research, Chiang Mai University, Chiang Mai 50200, Thailand
- Department of Oral Biology and Diagnostic Sciences, Faculty of Dentistry, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Nipon Chattipakorn
- Metabolomics Unit, Cardiac Electrophysiology Research and Training Center, Chiang Mai University, Chiang Mai 50200, Thailand;
- Center of Excellence in Cardiac Electrophysiology Research, Chiang Mai University, Chiang Mai 50200, Thailand
- Cardiac Electrophysiology Unit, Department of Physiology, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand
- Correspondence: (C.T.); (N.C.)
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Li M, Wen J. Recent progress in the application of omics technologies in the study of bio-mining microorganisms from extreme environments. Microb Cell Fact 2021; 20:178. [PMID: 34496835 PMCID: PMC8425152 DOI: 10.1186/s12934-021-01671-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Accepted: 08/30/2021] [Indexed: 11/11/2022] Open
Abstract
Bio-mining microorganisms are a key factor affecting the metal recovery rate of bio-leaching, which inevitably produces an extremely acidic environment. As a powerful tool for exploring the adaptive mechanisms of microorganisms in extreme environments, omics technologies can greatly aid our understanding of bio-mining microorganisms and their communities on the gene, mRNA, and protein levels. These omics technologies have their own advantages in exploring microbial diversity, adaptive evolution, changes in metabolic characteristics, and resistance mechanisms of single strains or their communities to extreme environments. These technologies can also be used to discover potential new genes, enzymes, metabolites, metabolic pathways, and species. In addition, integrated multi-omics analysis can link information at different biomolecular levels, thereby obtaining more accurate and complete global adaptation mechanisms of bio-mining microorganisms. This review introduces the current status and future trends in the application of omics technologies in the study of bio-mining microorganisms and their communities in extreme environments.
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Affiliation(s)
- Min Li
- Key Laboratory of Systems Bioengineering, Tianjin University, Tianjin, China.,Collaborative Innovation Center of Chemical Science and Engineering, Tianjin University, Tianjin, China.,Frontier Science Center of Ministry of Education, Tianjin University, Tianjin, China
| | - Jianping Wen
- Key Laboratory of Systems Bioengineering, Tianjin University, Tianjin, China. .,Collaborative Innovation Center of Chemical Science and Engineering, Tianjin University, Tianjin, China. .,Frontier Science Center of Ministry of Education, Tianjin University, Tianjin, China.
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Recovery and Enhanced Upgrading of Rare Earth Elements from Coal-Based Resources: Bioleaching and Precipitation. MINERALS 2021. [DOI: 10.3390/min11050484] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Rare earth elements (REEs) are of great importance to modern society and their reliable supply is a major concern of many industries that utilize them in metal alloys, semiconductors, electrical equipment, and defense equipment. REEs in the coal waste have been revealed to be an alternative resource for REEs production. In this study, the extraction, recovery, and upgrading of the REEs from coal waste has been realized with the bioleaching and precipitation processes. Reliable and sustainable acid and oxidant production from the oxidation of the pyrite with Acidithiobacillus ferrooxidans to generate acid for leaching were realized in this research. The acidified bioleaching solution was used to extract REEs from coal waste, with 13–14% yields for most REE elements (~72 h of leaching). However, recovery for longer duration tests was significant higher (varies from 40–60% for individual REEs). After extraction, precipitation and separation processes were designed with the aid of Visual Minteq calculations and modeling to concentrate the REEs. With the procedures designed in this research, a final REEs precipitate product containing 36.7% REEs was produced.
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Unraveling the Central Role of Sulfur-Oxidizing Acidiphilium multivorum LMS in Industrial Bioprocessing of Gold-Bearing Sulfide Concentrates. Microorganisms 2021; 9:microorganisms9050984. [PMID: 34062882 PMCID: PMC8147356 DOI: 10.3390/microorganisms9050984] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 04/19/2021] [Accepted: 04/29/2021] [Indexed: 11/16/2022] Open
Abstract
Acidiphilium multivorum LMS is an acidophile isolated from industrial bioreactors during the processing of the gold-bearing pyrite-arsenopyrite concentrate at 38–42 °C. Most strains of this species are obligate organoheterotrophs that do not use ferrous iron or reduced sulfur compounds as energy sources. However, the LMS strain was identified as one of the predominant sulfur oxidizers in acidophilic microbial consortia. In addition to efficient growth under strictly heterotrophic conditions, the LMS strain proved to be an active sulfur oxidizer both in the presence or absence of organic compounds. Interestingly, Ac. multivorum LMS was able to succeed more common sulfur oxidizers in microbial populations, which indicated a previously underestimated role of this bacterium in industrial bioleaching operations. In this study, the first draft genome of the sulfur-oxidizing Ac. multivorum was sequenced and annotated. Based on the functional genome characterization, sulfur metabolism pathways were reconstructed. The LMS strain possessed a complicated multi-enzyme system to oxidize elemental sulfur, thiosulfate, sulfide, and sulfite to sulfate as the final product. Altogether, the phenotypic description and genome analysis unraveled a crucial role of Ac. multivorum in some biomining processes and revealed unique strain-specific characteristics, including the ars genes conferring arsenic resistance, which are similar to those of phylogenetically distinct microorganisms.
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Unlocking Survival Mechanisms for Metal and Oxidative Stress in the Extremely Acidophilic, Halotolerant Acidihalobacter Genus. Genes (Basel) 2020; 11:genes11121392. [PMID: 33255299 PMCID: PMC7760498 DOI: 10.3390/genes11121392] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 11/20/2020] [Accepted: 11/22/2020] [Indexed: 12/22/2022] Open
Abstract
Microorganisms used for the biohydrometallurgical extraction of metals from minerals must be able to survive high levels of metal and oxidative stress found in bioleaching environments. The Acidihalobacter genus consists of four species of halotolerant, iron–sulfur-oxidizing acidophiles that are unique in their ability to tolerate chloride and acid stress while simultaneously bioleaching minerals. This paper uses bioinformatic tools to predict the genes and mechanisms used by Acidihalobacter members in their defense against a wide range of metals and oxidative stress. Analysis revealed the presence of multiple conserved mechanisms of metal tolerance. Ac. yilgarnensis F5T, the only member of this genus that oxidizes the mineral chalcopyrite, contained a 39.9 Kb gene cluster consisting of 40 genes encoding mobile elements and an array of proteins with direct functions in copper resistance. The analysis also revealed multiple strategies that the Acidihalobacter members can use to tolerate high levels of oxidative stress. Three of the Acidihalobacter genomes were found to contain genes encoding catalases, which are not common to acidophilic microorganisms. Of particular interest was a rubrerythrin genomic cluster containing genes that have a polyphyletic origin of stress-related functions.
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