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Nikolić N, Massaro S, Tagliapietra F, Squartini A, Schiavon S, Masin R. Method to evaluate the microbial degradation activity in silage, cow rumen with in vitro test, and in manure and slurry. MethodsX 2024; 12:102550. [PMID: 38283762 PMCID: PMC10820685 DOI: 10.1016/j.mex.2024.102550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 01/04/2024] [Indexed: 01/30/2024] Open
Abstract
Microorganisms are present everywhere and can influence a variety of processes. In agriculture and husbandry, the level of microbial activity can be crucial information, yet the methods for determining microbial activity are usually very long, complex, and costly. In this work, a novel and easy-to-use method, already in use for determining soil microbial activity, named Fertimetro was tested as a fast and cheap solution for measuring microbial activity in silages, in vitro rumen fluids, and manure and slurry. The method was adjusted for the specific conditions of the new testing environments. The results indicate that this method is adequate for measuring cellulolytic microbial activity in vitro rumen fluids, with a coefficient of repeatability (RT%) 92.2 at 24 h and 87.5 at 48 h, and also for cellulolytic microbial activity measures in manure RT% 39.0. While, due to the specific conditions in silages and slurry, this method is less adequate for measuring cellulolytic microbial activity in these environments. This work demonstrates that Fertimetro method can be used in different environments as an easy and cheaper alternative for measuring microbial activity, especially if the interest is only in quantifying the microbial activity and not in knowing the microbial species.1.Fertimetro is an easy-to-use and not costly method to evaluate microbial activity in different environments.2.This method is very adequate for measuring cellulolytic microbial activity in vitro rumen fluids and manure.
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Affiliation(s)
- Nebojša Nikolić
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, 35020 Legnaro, PD, Italy
| | - Selene Massaro
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, 35020 Legnaro, PD, Italy
| | - Franco Tagliapietra
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, 35020 Legnaro, PD, Italy
| | - Andrea Squartini
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, 35020 Legnaro, PD, Italy
| | - Stefano Schiavon
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, 35020 Legnaro, PD, Italy
| | - Roberta Masin
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, 35020 Legnaro, PD, Italy
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2
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Hossain TJ. Methods for screening and evaluation of antimicrobial activity: A review of protocols, advantages, and limitations. Eur J Microbiol Immunol (Bp) 2024; 14:97-115. [PMID: 38648108 PMCID: PMC11097785 DOI: 10.1556/1886.2024.00035] [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: 03/13/2024] [Accepted: 04/05/2024] [Indexed: 04/25/2024] Open
Abstract
Infectious diseases pose a formidable global challenge, compounded by the emergence of antimicrobial resistance. Consequently, researchers are actively exploring novel antimicrobial compounds as potential solutions. This endeavor underscores the pivotal role of methods employed for screening and evaluating antimicrobial activity-a critical step in discovery and characterization of antimicrobial agents. While traditional techniques such as well-diffusion, disk-diffusion, and broth-dilution are commonly utilized in antimicrobial assays, they may encounter limitations concerning reproducibility and speed. Additionally, a diverse array of antimicrobial assays including cross-streaking, poisoned-food, co-culture, time-kill kinetics, resazurin assay, bioautography, etc., are routinely employed in antimicrobial evaluations. Advanced techniques such as flow-cytometry, impedance analysis, and bioluminescent technique may offer rapid and sensitive results, providing deeper insights into the impact of antimicrobials on cellular integrity. However, their higher cost and limited accessibility in certain laboratory settings may present challenges. This article provides a comprehensive overview of assays designed to characterize antimicrobial activity, elucidating their underlying principles, protocols, advantages, and limitations. The primary objective is to enhance understanding of the methodologies designed for evaluating antimicrobial agents in our relentless battle against infectious diseases. By selecting the appropriate antimicrobial testing method, researchers can discern suitable conditions and streamline the identification of effective antimicrobial agents.
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Affiliation(s)
- Tanim Jabid Hossain
- Department of Biochemistry and Molecular Biology, University of Chittagong, Chattogram, Bangladesh
- Biochemistry and Pathogenesis of Microbes – BPM Unit, Laboratory for Health, Omics and Pathway Exploration (HOPE Research), Chattogram, Bangladesh
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3
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Vercammen H, Ondra M, Kotulova J, De La Hoz EC, Witters C, Jecmenova K, Le Compte M, Deben C, Ní Dhubhghaill S, Koppen C, Hajdúch M, Van den Bogerd B. "Keep on ROCKIn": Repurposed ROCK inhibitors to boost corneal endothelial regeneration. Biomed Pharmacother 2024; 174:116435. [PMID: 38513591 DOI: 10.1016/j.biopha.2024.116435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 03/06/2024] [Accepted: 03/15/2024] [Indexed: 03/23/2024] Open
Abstract
The global shortage of corneal endothelial graft tissue necessitates the exploration of alternative therapeutic strategies. Rho-associated protein kinase inhibitors (ROCKi), recognized for their regenerative potential in cardiology, oncology, and neurology, have shown promise in corneal endothelial regeneration. This study investigates the repurposing potential of additional ROCKi compounds. Through screening a self-assembled library of ROCKi on B4G12 corneal endothelial cells, we evaluated their dose-dependent effects on proliferation, migration, and toxicity using live-cell imaging. Nine ROCKi candidates significantly enhanced B4G12 proliferation compared to the basal growth rate. These candidates were further assessed for their potential to accelerate wound closure as another indicator for tissue regeneration capacity, with most demonstrating notable efficacy. To assess the potential impact of candidate ROCKi on key corneal endothelial cell markers related to cell proliferation, leaky tight junctions and ion efflux capacity, we analyzed the protein expression of cyclin E1, CDK2, p16, ZO-1 and Na+/K+-ATPase, respectively. Immunocytochemistry and western blot analysis confirmed the preservation of corneal endothelial markers post-treatment with ROCKi hits. However, notable cytoplasm enlargement and nuclear fragmentation were detected after the treatment with SR-3677 and Thiazovivin, indicating possible cellular stress. In compared parameters, Chroman-1 at a concentration of 10 nM outperformed other ROCKi, requiring significantly 1000-fold lower effective concentration than established ROCKi Y-27632 and Fasudil. Altogether, this study underscores the potential of repurposing ROCKi for treating corneal endothelial dysfunctions, offering a viable alternative to conventional grafting methods, and highlights Chroman-1 as a promising candidate structure for hit-to-lead development.
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Affiliation(s)
- Hendrik Vercammen
- Antwerp Research Group for Ocular Science (ARGOS), Translational Neurosciences, Faculty of Medicine and Health Sciences, University of Antwerp, Wilrijk, Belgium; Department of Ophthalmology, Antwerp University Hospital, Edegem, Belgium; DrugVision Lab, University of Antwerp, Wilrijk, Belgium.
| | - Martin Ondra
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University Olomouc, Olomouc, Czech Republic; Czech Advanced Technology and Research Institute (CATRIN), Palacky University Olomouc, Olomouc, Czech Republic
| | - Jana Kotulova
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University Olomouc, Olomouc, Czech Republic
| | | | - Charissa Witters
- Antwerp Research Group for Ocular Science (ARGOS), Translational Neurosciences, Faculty of Medicine and Health Sciences, University of Antwerp, Wilrijk, Belgium; Department of Ophthalmology, Antwerp University Hospital, Edegem, Belgium; DrugVision Lab, University of Antwerp, Wilrijk, Belgium
| | - Katerina Jecmenova
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University Olomouc, Olomouc, Czech Republic
| | | | | | | | - Carina Koppen
- Antwerp Research Group for Ocular Science (ARGOS), Translational Neurosciences, Faculty of Medicine and Health Sciences, University of Antwerp, Wilrijk, Belgium; Department of Ophthalmology, Antwerp University Hospital, Edegem, Belgium
| | - Marián Hajdúch
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University Olomouc, Olomouc, Czech Republic; Czech Advanced Technology and Research Institute (CATRIN), Palacky University Olomouc, Olomouc, Czech Republic
| | - Bert Van den Bogerd
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University Olomouc, Olomouc, Czech Republic; Czech Advanced Technology and Research Institute (CATRIN), Palacky University Olomouc, Olomouc, Czech Republic.
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4
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Facchini N, Wernli L, Rieken M, Bonkat G, Wirz D, Braissant O. Again and Again-Survival of Candida albicans in Urine Containing Antifungals. Pharmaceutics 2024; 16:605. [PMID: 38794267 PMCID: PMC11124869 DOI: 10.3390/pharmaceutics16050605] [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: 03/22/2024] [Revised: 04/25/2024] [Accepted: 04/26/2024] [Indexed: 05/26/2024] Open
Abstract
BACKGROUND Relapse of Candida albicans urinary tract infection (UTI) is frequent despite appropriate treatment, as commonly used antifungals such fluconazole and flucytosine are only fungistatics. To improve treatment of Candida UTI and decrease relapses, understanding the long-term metabolic activity and survival of C. albicans in urine containing antifungals at minimal inhibitory concentration (MIC) is needed. METHODS we monitored the survival, metabolic activity and consumption of glucose and proteins by C. albicans using conventional methods and isothermal microcalorimetry (IMC). We also investigated the influence of dead Candida cells on the growth of their living counterparts. RESULTS For 33 days, weak activity was observed in samples containing antifungals in which C. albicans growth rate was reduced by 48%, 60% and 88%, and the lag increased to 172 h, 168 h and 6 h for amphotericin, flucytosine and fluconazole, respectively. The metabolic activity peaks corresponded to the plate counts but were delayed compared to the exhaustion of resources. The presence of dead cells promoted growth in artificial urine, increasing growth rate and reducing lag in similar proportions. CONCLUSIONS Even with antifungal treatment, C. albicans relapses are possible. The low metabolic activity of surviving cells leading to regrowth and chlamydospore formation possibly supported by autophagy are likely important factors in relapses.
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Affiliation(s)
- Nevio Facchini
- Department of Biomedical Engineering, University of Basel, Hegenheimermattweg 167B/C, 4123 Allschwil, Switzerland; (N.F.)
- Faculty of Medicine, University of Basel, Klingelbergstrasse 61, 4056 Basel, Switzerland
| | - Lukas Wernli
- Department of Biomedical Engineering, University of Basel, Hegenheimermattweg 167B/C, 4123 Allschwil, Switzerland; (N.F.)
- Department of Urology, Kantonsspital Baselland, Rheinstrasse 26, 4410 Liestal, Switzerland
| | - Malte Rieken
- Faculty of Medicine, University of Basel, Klingelbergstrasse 61, 4056 Basel, Switzerland
- alta uro AG, Centralbahnplatz 6, 4051 Basel, Switzerland
| | - Gernot Bonkat
- Faculty of Medicine, University of Basel, Klingelbergstrasse 61, 4056 Basel, Switzerland
- alta uro AG, Centralbahnplatz 6, 4051 Basel, Switzerland
| | - Dieter Wirz
- Department of Biomedical Engineering, University of Basel, Hegenheimermattweg 167B/C, 4123 Allschwil, Switzerland; (N.F.)
| | - Olivier Braissant
- Department of Biomedical Engineering, University of Basel, Hegenheimermattweg 167B/C, 4123 Allschwil, Switzerland; (N.F.)
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Gevorgyan H, Baghdasaryan L, Trchounian K. Regulation of metabolism and proton motive force generation during mixed carbon fermentation by an Escherichia coli strain lacking the F OF 1-ATPase. BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2024; 1865:149034. [PMID: 38354879 DOI: 10.1016/j.bbabio.2024.149034] [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: 10/03/2023] [Revised: 01/15/2024] [Accepted: 02/09/2024] [Indexed: 02/16/2024]
Abstract
Proton FOF1-ATPase is the key enzyme in E. coli under fermentative conditions. In this study the role of E. coli proton ATPase in the μ and formation of metabolic pathways during the fermentation of mixture of glucose, glycerol and formate using the DK8 (lacking FOF1) mutant strain was investigated. It was shown that the contribution of FOF1-ATPase in the specific growth rate was ∼45 %. Formate was not taken up in the DK8 strain during the initial hours of the growth. The utilization rates of glucose and glycerol were unchanged in DK8, however, the production of succinate, lactate and ethanol was decreased causing a reduction of the redox state up to -450 mV. Moreover, the contribution of FOF1-ATPase in the interplay between H+ and H2 cycles was described depending on the bacterial growth phase and main utilizing substrate. Besides, the H2 production rate in the DK8 strain was decreased by ∼60 % at 20 h and was absent at 72 h. Δp was decreased from -157 ± 4.8 mV to -140 ± 4.2 mV at 20 h and from -195 ± 5.9 mV to -148 ± 4.4 mV at 72 h, compared to WT. Taken together it can be concluded that during fermentation of mixed carbon sources metabolic cross talk between FOF1-ATPase-TrkA-Hyd-Fdh-H is taking place for maintaining the cell energy balance via regulation proton motive force.
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Affiliation(s)
- Heghine Gevorgyan
- Department of Biochemistry, Microbiology and Biotechnology, Faculty of Biology, Yerevan State University, 0025 Yerevan, Armenia; Scientific-Research Institute of Biology, Faculty of Biology, Yerevan State University, 0025 Yerevan, Armenia; Microbial Biotechnologies and Biofuel Innovation Center, Yerevan State University, 0025 Yerevan, Armenia
| | - Lilit Baghdasaryan
- Department of Biochemistry, Microbiology and Biotechnology, Faculty of Biology, Yerevan State University, 0025 Yerevan, Armenia; Microbial Biotechnologies and Biofuel Innovation Center, Yerevan State University, 0025 Yerevan, Armenia
| | - Karen Trchounian
- Department of Biochemistry, Microbiology and Biotechnology, Faculty of Biology, Yerevan State University, 0025 Yerevan, Armenia; Scientific-Research Institute of Biology, Faculty of Biology, Yerevan State University, 0025 Yerevan, Armenia; Microbial Biotechnologies and Biofuel Innovation Center, Yerevan State University, 0025 Yerevan, Armenia.
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6
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Herman TS, da Silva Goersch C, Bocca AL, Fernandes L. Resazurin to determine the minimum inhibitory concentration on antifungal susceptibility assays for Fonsecaea sp. using a modified EUCAST protocol. Braz J Microbiol 2024:10.1007/s42770-024-01293-2. [PMID: 38438831 DOI: 10.1007/s42770-024-01293-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 02/27/2024] [Indexed: 03/06/2024] Open
Abstract
Chromoblastomycosis is a fungal chronic disease, which affects humans, especially in cutaneous and subcutaneous tissues. There is no standard treatment for Chromoblastomycosis, and it is a therapeutic challenge, due natural resistance of their causative agents, inadequate response of patients and common cases of relapse. Protocols for determination of antifungal drugs susceptibility are not standardized for chromoblastomycosis agents and endpoint definition is usually based on visual inspection, which depends on the analyst, making it sometimes inaccurate. We presented a colorimetric and quantitative methodology based on resazurin reduction to resofurin to determine the metabolic status of viable cells of Fonsecaea sp. Performing antifungal susceptibility assay by a modified EUCAST protocol allied to resazurin, we validated the method to identify the minimum inhibitory concentrations of itraconazole, fluconazole, amphotericin B, and terbinafine for eight Fonsecaea clinical isolates. According to our data, resazurin is a good indicator of metabolic status of viable cells, including those exposed to antifungal drugs. This work aimed to test resazurin as an indicator of the metabolic activity of Fonsecaea species in susceptibility assays to antifungal drugs. Species of this genus are the main causative agents of Chromoblastomycosis, which affects humans.
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Affiliation(s)
- Tatiana Sobianski Herman
- Postgraduate Program in Molecular Pathology, Faculty of Medicine, University of Brasília, UnB, Brasília, DF, Brazil
- Laboratory of Applied Immunology, Department of Cell Biology, Institute of Biological Sciences, University of Brasília, UnB, Room J1 28/8, Brasília, DF, 70910-900, Brazil
| | - Camila da Silva Goersch
- Laboratory of Applied Immunology, Department of Cell Biology, Institute of Biological Sciences, University of Brasília, UnB, Room J1 28/8, Brasília, DF, 70910-900, Brazil
- Postgraduate Program in Microbial Biology, Institute of Biological Science, University of Brasília, UnB, Brasília, DF, Brazil
| | - Anamelia Lorenzetti Bocca
- Postgraduate Program in Molecular Pathology, Faculty of Medicine, University of Brasília, UnB, Brasília, DF, Brazil
- Laboratory of Applied Immunology, Department of Cell Biology, Institute of Biological Sciences, University of Brasília, UnB, Room J1 28/8, Brasília, DF, 70910-900, Brazil
| | - Larissa Fernandes
- Laboratory of Applied Immunology, Department of Cell Biology, Institute of Biological Sciences, University of Brasília, UnB, Room J1 28/8, Brasília, DF, 70910-900, Brazil.
- Postgraduate Program in Microbial Biology, Institute of Biological Science, University of Brasília, UnB, Brasília, DF, Brazil.
- Faculty of Ceilândia, University of Brasília, UnB, Brasília, DF, Brazil.
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7
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Zaragoza N, Anderson GI, Allison-Logan S, Monir K, Furst AL. Novel delivery systems for controlled release of bacterial therapeutics. Trends Biotechnol 2024:S0167-7799(24)00002-7. [PMID: 38310020 DOI: 10.1016/j.tibtech.2024.01.002] [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: 11/13/2023] [Revised: 01/09/2024] [Accepted: 01/09/2024] [Indexed: 02/05/2024]
Abstract
As more is learned about the benefits of microbes, their potential to prevent and treat disease is expanding. Microbial therapeutics are less burdensome and costly to produce than traditional molecular drugs, often with superior efficacy. Yet, as with most medicines, controlled dosing and delivery to the area of need remain key challenges for microbes. Advances in materials to control small-molecule delivery are expected to translate to microbes, enabling similar control with equivalent benefits. In this perspective, recent advances in living biotherapeutics are discussed within the context of new methods for their controlled release. The integration of these advances provides a roadmap for the design, synthesis, and analysis of controlled microbial therapeutic delivery systems.
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Affiliation(s)
- Nadia Zaragoza
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Grace I Anderson
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Stephanie Allison-Logan
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Kirmina Monir
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Ariel L Furst
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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8
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de Souza MQ, Bierhals DV, Reis AJ, Chimara E, Vianna JS, von Groll A, da Silva PA, Ramis IB. 2,3,5-triphenyl tetrazolium chloride as colorimetric indicator for drug susceptibility testing against nontuberculous mycobacteria. Diagn Microbiol Infect Dis 2024; 108:116096. [PMID: 37931387 DOI: 10.1016/j.diagmicrobio.2023.116096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 09/04/2023] [Accepted: 09/22/2023] [Indexed: 11/08/2023]
Abstract
This study aimed to propose and evaluate a drug susceptibility testing (DST) using the 2,3,5-triphenyl tetrazolium chloride (TTC) as a colorimetric indicator against Mycobacterium abscessus complex (MABC), M. avium complex (MAC), and M. kansasii strains, main nontuberculous mycobacteria (NTM) of clinical relevance. Our results demonstrated that the assay using TTC and the broth microdilution method recommended by the Clinical and Laboratory Standards Institute had essential agreement above 91%, 92%, and 100%, for drugs tested against MABC, MAC, and M. kansasii strains, respectively. Categorical agreement above 91% was obtained for most drugs tested against MABC, except to cefoxitin (76.5%). For drugs tested against MAC and M. kansasii, categorical agreement above 92% and 100% was observed, respectively. TTC showed to be a promising colorimetric indicator of growth to be used in DST for NTM, allowing an easier reading of results.
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Affiliation(s)
- Mariana Quaresma de Souza
- Laboratório de Micobactérias, Núcleo de Pesquisa em Microbiologia Médica, Programa de Pós-Graduação em Ciências da Saúde, Faculdade de Medicina, Universidade Federal do Rio Grande, Rio Grande, Rio Grande do Sul, Brazil
| | - Dienefer Venske Bierhals
- Laboratório de Micobactérias, Núcleo de Pesquisa em Microbiologia Médica, Programa de Pós-Graduação em Ciências da Saúde, Faculdade de Medicina, Universidade Federal do Rio Grande, Rio Grande, Rio Grande do Sul, Brazil
| | - Ana Julia Reis
- Laboratório de Micobactérias, Núcleo de Pesquisa em Microbiologia Médica, Programa de Pós-Graduação em Ciências da Saúde, Faculdade de Medicina, Universidade Federal do Rio Grande, Rio Grande, Rio Grande do Sul, Brazil
| | - Erica Chimara
- Núcleo de Tuberculose e Micobacterioses, Instituto Adolfo Lutz, São Paulo, Brazil
| | - Júlia Silveira Vianna
- Laboratório de Micobactérias, Núcleo de Pesquisa em Microbiologia Médica, Programa de Pós-Graduação em Ciências da Saúde, Faculdade de Medicina, Universidade Federal do Rio Grande, Rio Grande, Rio Grande do Sul, Brazil
| | - Andrea von Groll
- Laboratório de Micobactérias, Núcleo de Pesquisa em Microbiologia Médica, Programa de Pós-Graduação em Ciências da Saúde, Faculdade de Medicina, Universidade Federal do Rio Grande, Rio Grande, Rio Grande do Sul, Brazil
| | - Pedro Almeida da Silva
- Laboratório de Micobactérias, Núcleo de Pesquisa em Microbiologia Médica, Programa de Pós-Graduação em Ciências da Saúde, Faculdade de Medicina, Universidade Federal do Rio Grande, Rio Grande, Rio Grande do Sul, Brazil.
| | - Ivy Bastos Ramis
- Laboratório de Micobactérias, Núcleo de Pesquisa em Microbiologia Médica, Programa de Pós-Graduação em Ciências da Saúde, Faculdade de Medicina, Universidade Federal do Rio Grande, Rio Grande, Rio Grande do Sul, Brazil
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9
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Dalal N, Makharia GK, Dalal M, Mohan A, Singh R, Kumar A. Gut Metabolite Indoxyl Sulfate Has Selective Deleterious and Anticancer Effect on Colon Cancer Cells. J Med Chem 2023; 66:17074-17085. [PMID: 38103027 DOI: 10.1021/acs.jmedchem.3c01907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2023]
Abstract
There are a number of reports about anticancer activity of indole derivatives. In this study, we investigated the role of indoxyl sulfate (IS) for its selective anticancer activity on colon cancer cells. IS treatment on HCT-116 and HT-29 human epithelial adenocarcinoma cells led to a decrease in cell proliferation, cell viability, and ATP content. Colon cancer cells showed a 10% increase in cell apoptosis in comparison to control. Due to IS treatment, cell morphology got distorted, cell number found decreased, intracellular vesicles formed, and cells were found floating in the media. Cells also showed a loss in membrane integrity and a decrease in colony-forming ability and ceased at the G2/M phase of the cell cycle. No significant change was noted in the level of inflammatory cytokines IL-17A, IL-1β, and TNF-α, histology, length of intestine, and spleen after 100 mM IS treatment to balb/c mice. These observations indicate the selective anticancer effect of IS on colon cancer cells.
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Affiliation(s)
- Nishu Dalal
- Gene Regulation Laboratory, National Institute of Immunology, New Delhi 110067, India
- Department of Environmental Studies, Satyawati College, Delhi University, Delhi 110052, India
| | - Govind K Makharia
- Department of Gastroenterology and Human Nutrition, AIIMS, New Delhi 110029, India
| | - Monu Dalal
- ICMR - National Institute of Malaria Research, New Delhi 110077, India
| | - Anand Mohan
- School of Bioengineering and Biosciences, Lovely Professional University, Phagwara 144411, Punjab, India
| | - Rajeev Singh
- Department of Environmental Studies, Satyawati College, Delhi University, Delhi 110052, India
| | - Anil Kumar
- Gene Regulation Laboratory, National Institute of Immunology, New Delhi 110067, India
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10
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Kassem A, Abbas L, Coutinho O, Opara S, Najaf H, Kasperek D, Pokhrel K, Li X, Tiquia-Arashiro S. Applications of Fourier Transform-Infrared spectroscopy in microbial cell biology and environmental microbiology: advances, challenges, and future perspectives. Front Microbiol 2023; 14:1304081. [PMID: 38075889 PMCID: PMC10703385 DOI: 10.3389/fmicb.2023.1304081] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 11/03/2023] [Indexed: 01/02/2024] Open
Abstract
Microorganisms play pivotal roles in shaping ecosystems and biogeochemical cycles. Their intricate interactions involve complex biochemical processes. Fourier Transform-Infrared (FT-IR) spectroscopy is a powerful tool for monitoring these interactions, revealing microorganism composition and responses to the environment. This review explores the diversity of applications of FT-IR spectroscopy within the field of microbiology, highlighting its specific utility in microbial cell biology and environmental microbiology. It emphasizes key applications such as microbial identification, process monitoring, cell wall analysis, biofilm examination, stress response assessment, and environmental interaction investigation, showcasing the crucial role of FT-IR in advancing our understanding of microbial systems. Furthermore, we address challenges including sample complexity, data interpretation nuances, and the need for integration with complementary techniques. Future prospects for FT-IR in environmental microbiology include a wide range of transformative applications and advancements. These include the development of comprehensive and standardized FT-IR libraries for precise microbial identification, the integration of advanced analytical techniques, the adoption of high-throughput and single-cell analysis, real-time environmental monitoring using portable FT-IR systems and the incorporation of FT-IR data into ecological modeling for predictive insights into microbial responses to environmental changes. These innovative avenues promise to significantly advance our understanding of microorganisms and their complex interactions within various ecosystems.
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Affiliation(s)
- Amin Kassem
- Department of Natural Sciences, University of Michigan-Dearborn, Dearborn, MI, United States
| | - Lana Abbas
- Department of Natural Sciences, University of Michigan-Dearborn, Dearborn, MI, United States
| | - Oliver Coutinho
- Department of Natural Sciences, University of Michigan-Dearborn, Dearborn, MI, United States
| | - Somie Opara
- Department of Natural Sciences, University of Michigan-Dearborn, Dearborn, MI, United States
| | - Hawraa Najaf
- Department of Natural Sciences, University of Michigan-Dearborn, Dearborn, MI, United States
| | - Diana Kasperek
- Department of Natural Sciences, University of Michigan-Dearborn, Dearborn, MI, United States
| | - Keshav Pokhrel
- Department of Mathematics and Statistics, University of Michigan-Dearborn, Dearborn, MI, United States
| | - Xiaohua Li
- Department of Natural Sciences, University of Michigan-Dearborn, Dearborn, MI, United States
| | - Sonia Tiquia-Arashiro
- Department of Natural Sciences, University of Michigan-Dearborn, Dearborn, MI, United States
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11
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Huang S, Qin H, Liu M. Photoinactivation of Escherichia coli by 405 nm and 450 nm light-emitting diodes: Comparison of continuous wave and pulsed light. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY. B, BIOLOGY 2023; 248:112799. [PMID: 37832394 DOI: 10.1016/j.jphotobiol.2023.112799] [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: 04/04/2023] [Revised: 07/12/2023] [Accepted: 10/05/2023] [Indexed: 10/15/2023]
Abstract
BACKGROUND Antimicrobial blue light (ABL) therapy is one of the novel non-antibiotic approaches and recent studies showed the potential of pulsed ABL. PURPOSE Comparing photoinactivation effect of continuous wave (CW) and pulsed blue light and investigating the impact of varying light parameters. METHODS E. coli cells in planktonic were treated with CW and pulsed light (405 nm and 450 nm) at 60 mW/cm2, and the samples were taken to assess survival, reactive oxygen species (ROS) level, damage of cell membrane and metabolic activity. Further, a ROS scavenger was used to find the role of ROS played in ABL therapy. RESULTS E. coli was more sensitive to 405 nm light and the photoinactivation was dose-dependent. Pulsed 405 nm light showed the better antimicrobial effect on E. coli and caused increasing damage of cell membrane. It might be attributed to the ROS production in bacteria. CONCLUSION Pulsed light has a potential of improving the efficacy of ABL therapy and is worth to be explored deeply further.
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Affiliation(s)
- Shijie Huang
- School of Information Science and Technology, Fudan University, 2005th Songhu Road, Shanghai 200438, China
| | - Haokuan Qin
- Academy for Engineering and Technology, Fudan University, 220th Handan Road, Shanghai 200433, China
| | - Muqing Liu
- School of Information Science and Technology, Fudan University, 2005th Songhu Road, Shanghai 200438, China; Zhongshan Fudan Joint Innovation Center, 6th Xiangxing Rd, Zhongshan City 528403, China.
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12
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Kostešić E, Mitrović M, Kajan K, Marković T, Hausmann B, Orlić S, Pjevac P. Microbial Diversity and Activity of Biofilms from Geothermal Springs in Croatia. MICROBIAL ECOLOGY 2023; 86:2305-2319. [PMID: 37209180 PMCID: PMC10640420 DOI: 10.1007/s00248-023-02239-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 05/07/2023] [Indexed: 05/22/2023]
Abstract
Hot spring biofilms are stable, highly complex microbial structures. They form at dynamic redox and light gradients and are composed of microorganisms adapted to the extreme temperatures and fluctuating geochemical conditions of geothermal environments. In Croatia, a large number of poorly investigated geothermal springs host biofilm communities. Here, we investigated the microbial community composition of biofilms collected over several seasons at 12 geothermal springs and wells. We found biofilm microbial communities to be temporally stable and highly dominated by Cyanobacteria in all but one high-temperature sampling site (Bizovac well). Of the physiochemical parameters recorded, temperature had the strongest influence on biofilm microbial community composition. Besides Cyanobacteria, the biofilms were mainly inhabited by Chloroflexota, Gammaproteobacteria, and Bacteroidota. In a series of incubations with Cyanobacteria-dominated biofilms from Tuhelj spring and Chloroflexota- and Pseudomonadota-dominated biofilms from Bizovac well, we stimulated either chemoorganotrophic or chemolithotrophic community members, to determine the fraction of microorganisms dependent on organic carbon (in situ predominantly produced via photosynthesis) versus energy derived from geochemical redox gradients (here simulated by addition of thiosulfate). We found surprisingly similar levels of activity in response to all substrates in these two distinct biofilm communities, and observed microbial community composition and hot spring geochemistry to be poor predictors of microbial activity in the study systems.
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Affiliation(s)
- Ema Kostešić
- Division of Materials Chemistry, Ruđer Bošković Institute, Zagreb, Croatia
| | - Maja Mitrović
- Division of Materials Chemistry, Ruđer Bošković Institute, Zagreb, Croatia
| | - Katarina Kajan
- Division of Materials Chemistry, Ruđer Bošković Institute, Zagreb, Croatia
- Center of Excellence for Science and Technology-Integration of Mediterranean Region (STIM), Split, Croatia
| | | | - Bela Hausmann
- Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, Vienna, Austria
- Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria
| | - Sandi Orlić
- Division of Materials Chemistry, Ruđer Bošković Institute, Zagreb, Croatia
- Center of Excellence for Science and Technology-Integration of Mediterranean Region (STIM), Split, Croatia
| | - Petra Pjevac
- Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, Vienna, Austria.
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria.
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13
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Shajib MS, Futrega K, Davies AM, Franco RAG, McKenna E, Guillesser B, Klein TJ, Crawford RW, Doran MR. A tumour-spheroid manufacturing and cryopreservation process that yields a highly reproducible product ready for direct use in drug screening assays. J R Soc Interface 2023; 20:20230468. [PMID: 37817581 PMCID: PMC10565407 DOI: 10.1098/rsif.2023.0468] [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: 05/01/2023] [Accepted: 09/11/2023] [Indexed: 10/12/2023] Open
Abstract
If it were possible to purchase tumour-spheroids as a standardised product, ready for direct use in assays, this may contribute to greater research reproducibility, potentially reducing costs and accelerating outcomes. Herein, we describe a workflow where uniformly sized cancer tumour-spheroids are mass-produced using microwell culture, cryopreserved with high viability, and then cultured in neutral buoyancy media for drug testing. C4-2B prostate cancer or MCF-7 breast cancer cells amalgamated into uniform tumour-spheroids after 48 h of culture. Tumour-spheroids formed from 100 cells each tolerated the cryopreservation process marginally better than tumour-spheroids formed from 200 or 400 cells. Post-thaw, tumour-spheroid metabolic activity was significantly reduced, suggesting mitochondrial damage. Metabolic function was rescued by thawing the tumour-spheroids into medium supplemented with 10 µM N-Acetyl-l-cysteine (NAC). Following thaw, the neutral buoyancy media, Happy Cell ASM, was used to maintain tumour-spheroids as discrete tissues during drug testing. Fresh and cryopreserved C4-2B or MCF-7 tumour-spheroids responded similarly to titrations of Docetaxel. This protocol will contribute to a future where tumour-spheroids may be available for purchase as reliable and reproducible products, allowing laboratories to efficiently replicate and build on published research, in many cases, making tumour-spheroids simply another cell culture reagent.
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Affiliation(s)
- Md. Shafiullah Shajib
- School of Biomedical Science, Faculty of Health, Queensland University of Technology (QUT), Brisbane, Queensland, Australia
- Translational Research Institute, Brisbane, Queensland, Australia
| | - Kathryn Futrega
- Centre for Biomedical Technologies, School of Mechanical, Medical, and Process Engineering, Faculty of Engineering, Queensland University of Technology (QUT), Brisbane, Queensland, Australia
- Translational Research Institute, Brisbane, Queensland, Australia
- Department of Health and Human Services, National Institute of Dental and Craniofacial Research (NIDCR), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Anthony M. Davies
- Translational Research Institute, Brisbane, Queensland, Australia
- Vale Life Sciences, Brisbane, Australia
| | - Rose Ann G. Franco
- Centre for Biomedical Technologies, School of Mechanical, Medical, and Process Engineering, Faculty of Engineering, Queensland University of Technology (QUT), Brisbane, Queensland, Australia
- Translational Research Institute, Brisbane, Queensland, Australia
| | - Eamonn McKenna
- Centre for Biomedical Technologies, School of Mechanical, Medical, and Process Engineering, Faculty of Engineering, Queensland University of Technology (QUT), Brisbane, Queensland, Australia
- Translational Research Institute, Brisbane, Queensland, Australia
| | - Bianca Guillesser
- School of Biomedical Science, Faculty of Health, Queensland University of Technology (QUT), Brisbane, Queensland, Australia
- Centre for Biomedical Technologies, School of Mechanical, Medical, and Process Engineering, Faculty of Engineering, Queensland University of Technology (QUT), Brisbane, Queensland, Australia
- Translational Research Institute, Brisbane, Queensland, Australia
| | - Travis J. Klein
- Centre for Biomedical Technologies, School of Mechanical, Medical, and Process Engineering, Faculty of Engineering, Queensland University of Technology (QUT), Brisbane, Queensland, Australia
| | - Ross W. Crawford
- Centre for Biomedical Technologies, School of Mechanical, Medical, and Process Engineering, Faculty of Engineering, Queensland University of Technology (QUT), Brisbane, Queensland, Australia
| | - Michael R. Doran
- School of Biomedical Science, Faculty of Health, Queensland University of Technology (QUT), Brisbane, Queensland, Australia
- Centre for Biomedical Technologies, School of Mechanical, Medical, and Process Engineering, Faculty of Engineering, Queensland University of Technology (QUT), Brisbane, Queensland, Australia
- Translational Research Institute, Brisbane, Queensland, Australia
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Marcos-Fernández R, Sánchez B, Ruiz L, Margolles A. Convergence of flow cytometry and bacteriology. Current and future applications: a focus on food and clinical microbiology. Crit Rev Microbiol 2023; 49:556-577. [PMID: 35749433 DOI: 10.1080/1040841x.2022.2086035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 05/12/2022] [Accepted: 05/31/2022] [Indexed: 11/03/2022]
Abstract
Since its development in the 1960s, flow cytometry (FCM) was quickly revealed a powerful tool to analyse cell populations in medical studies, yet, for many years, was almost exclusively used to analyse eukaryotic cells. Instrument and methodological limitations to distinguish genuine bacterial signals from the background, among other limitations, have hampered FCM applications in bacteriology. In recent years, thanks to the continuous development of FCM instruments and methods with a higher discriminatory capacity to detect low-size particles, FCM has emerged as an appealing technique to advance the study of microbes, with important applications in research, clinical and industrial settings. The capacity to rapidly enumerate and classify individual bacterial cells based on viability facilitates the monitoring of bacterial presence in foodstuffs or clinical samples, reducing the time needed to detect contamination or infectious processes. Besides, FCM has stood out as a valuable tool to advance the study of complex microbial communities, or microbiomes, that are very relevant in the context of human health, as well as to understand the interaction of bacterial and host cells. This review highlights current developments in, and future applications of, FCM in bacteriology, with a focus on those related to food and clinical microbiology.
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Affiliation(s)
- Raquel Marcos-Fernández
- Department of Microbiology and Biochemistry of Dairy Products, Dairy Research Institute of Asturias, Spanish National Research Council (IPLA-CSIC), Asturias, Spain
- Functionality and Ecology of Beneficial Microbes (MicroHealth) Group, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Asturias, Spain
| | - Borja Sánchez
- Department of Microbiology and Biochemistry of Dairy Products, Dairy Research Institute of Asturias, Spanish National Research Council (IPLA-CSIC), Asturias, Spain
- Functionality and Ecology of Beneficial Microbes (MicroHealth) Group, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Asturias, Spain
| | - Lorena Ruiz
- Department of Microbiology and Biochemistry of Dairy Products, Dairy Research Institute of Asturias, Spanish National Research Council (IPLA-CSIC), Asturias, Spain
- Functionality and Ecology of Beneficial Microbes (MicroHealth) Group, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Asturias, Spain
| | - Abelardo Margolles
- Department of Microbiology and Biochemistry of Dairy Products, Dairy Research Institute of Asturias, Spanish National Research Council (IPLA-CSIC), Asturias, Spain
- Functionality and Ecology of Beneficial Microbes (MicroHealth) Group, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Asturias, Spain
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15
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Sychev AV, Lavrova AI, Dogonadze MZ, Postnikov EB. Establishing Compliance between Spectral, Colourimetric and Photometric Indicators in Resazurin Reduction Test. Bioengineering (Basel) 2023; 10:962. [PMID: 37627847 PMCID: PMC10451944 DOI: 10.3390/bioengineering10080962] [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: 06/19/2023] [Revised: 08/09/2023] [Accepted: 08/10/2023] [Indexed: 08/27/2023] Open
Abstract
The resazurin reduction test is one of the basic tests for bacterial culture viability and drug resistance endorsed by the World Health Organisation. At the same time, conventional spectrophotometric and spectrofluorimetric methods demand rather bulky and expensive equipment. This induces a challenge for developing simpler approaches to sensor systems that are portable and applicable in resource-limited settings. In this work, we address two such alternative approaches, based on the colour processing of the microbiological plate's photographic images and single-channel photometry with a recently developed portable microbiological analyser. The key results consist of establishing a sequential linear correspondence between the concentration of resorufin produced due to the reduction of resazurin by viable bacteria as determined by the UV-Vis studies, the intensity of the a* channel of the CIE L*a*b* colour space and the transmitted light intensity registered by a luxmeter under the LED illumination with a yellow colour filter. This route is illustrated with the chemical system "Hydrazine hydrate - resazurin", isolating the target colour change-inducing reaction and the test of determining the minimal inhibition concentration of the antibacterial first-line drug isoniazid acting on the culture of the H37Rv strain of M. tuberculosis.
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Affiliation(s)
- Alexander V. Sychev
- Research Center for Condensed Matter Physics, Kursk State University, Radishcheva St. 33, 305000 Kursk, Russia
| | - Anastasia I. Lavrova
- Saint-Petersburg State Research Institute of Phthisiopulmonology, Lygovsky av. 2-4, 191036 Saint-Petersburg, Russia
- Faculty of Medicine, Saint-Petersburg State University, Universitetskaya emb 7-9, 199034 Saint-Petersburg, Russia
| | - Marine Z. Dogonadze
- Saint-Petersburg State Research Institute of Phthisiopulmonology, Lygovsky av. 2-4, 191036 Saint-Petersburg, Russia
| | - Eugene B. Postnikov
- Department of Theoretical Physics, Kursk State University, Radishcheva St. 33, 305000 Kursk, Russia
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16
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Urbaniec J, Sanderson-Smith M, McFadden J, Hai FI, Hingley-Wilson SM. Dysregulated NAD(H) homeostasis associated with ciprofloxacin tolerance in Escherichia coli investigated on a single-cell level with the Peredox [NADH:NAD+] biosensor. Front Microbiol 2023; 14:1191968. [PMID: 37415820 PMCID: PMC10321300 DOI: 10.3389/fmicb.2023.1191968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 05/11/2023] [Indexed: 07/08/2023] Open
Abstract
Introduction Antibiotic persistence (subpopulation tolerance) occurs when a subpopulation of antibiotic sensitive cells survives prolonged exposure to a bactericidal concentration of an antibiotic, and is capable of regrowth once the antibiotic is removed. This phenomenon has been shown to contribute to prolonged treatment duration, infection recurrence, and accelerated development of genetic resistance. Currently, there are no biomarkers which would allow for segregation of these antibiotic-tolerant cells from the bulk population prior to antibiotic exposure, limiting research on this phenomenon to retrograde analyses. However, it has been previously shown that persisters often have a dysregulated intracellular redox homeostasis, warranting its investigation as a potential marker for antibiotic tolerance. Furthermore, it is currently unknown whether another antibiotic tolerant subpopulation - viable but non-culturable cells (VBNCs), are simply persisters with extreme lag phase, or are formed through separate pathways. VBNCs similarly to persisters remain viable following antibiotic exposure, however, are not capable of regrowth in standard conditions. Methods In this article we employed an NADH:NAD+ biosensor (Peredox) to investigate NADH homeostasis of ciprofloxacin-tolerant E. coli cells on a single-cell level. [NADH:NAD+] was used as a proxy for measuring intracellular redox homeostasis and respiration rate. Results and Discussion First, we demonstrated that ciprofloxacin exposure results in a high number of VBNCs, several orders of magnitude higher than persisters. However, we found no correlation in the frequencies of persister and VBNC subpopulations. Ciprofloxacin-tolerant cells (persisters & VBNCs) were actively undergoing respiration, although at a significantly lower rate on average when compared to the bulk population. We also noted significant heterogeneity on a single-cell level within the subpopulations, however were unable to segregate persisters from VBNCs based on these observations alone. Finally, we showed that in the highly-persistent strain of E. coli, E. coli HipQ, ciprofloxacin-tolerant cells have a significantly lower [NADH:NAD+] ratio than tolerant cells of its parental strain, providing further link between disturbed NADH homeostasis and antibiotic tolerance.
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Affiliation(s)
- Joanna Urbaniec
- Department of Microbial Sciences, University of Surrey, Guildford, United Kingdom
- School of Civil, Mining and Environmental Engineering, University of Wollongong, Wollongong, NSW, Australia
- School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW, Australia
| | - Martina Sanderson-Smith
- School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW, Australia
| | - Johnjoe McFadden
- Department of Microbial Sciences, University of Surrey, Guildford, United Kingdom
| | - Faisal I. Hai
- School of Civil, Mining and Environmental Engineering, University of Wollongong, Wollongong, NSW, Australia
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Matulis D, Wadsö L, Fahmy K. Special Issue "Advances in Monitoring Metabolic Activities of Microorganisms by Calorimetry". Microorganisms 2023; 11:1204. [PMID: 37317176 DOI: 10.3390/microorganisms11051204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Accepted: 04/20/2023] [Indexed: 06/16/2023] Open
Abstract
In recent decades, the calorimetric monitoring of microbial metabolism, i [...].
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Affiliation(s)
- Daumantas Matulis
- Life Sciences Center, Vilnius University, Saulėtekio al. 7, 10257 Vilnius, Lithuania
| | - Lars Wadsö
- Division of Building Materials, Lund University, Box 118, 221 00 Lund, Sweden
| | - Karim Fahmy
- Department of Biophysics, Helmholtz-Zentrum Dresden-Rossendorf, Bautzner Landstrasse 400, 01328 Dresden, Germany
- Cluster of Excellence Physics of Life, Technische Universität Dresden, Arnoldstraße 18, 01307 Dresden, Germany
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18
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VanderWal AR, Park JU, Polevoda B, Nicosia JK, Vargas AMM, Kellogg EH, O’Connell MR. Csx28 is a membrane pore that enhances CRISPR-Cas13b-dependent antiphage defense. Science 2023; 380:410-415. [PMID: 37104586 PMCID: PMC10228660 DOI: 10.1126/science.abm1184] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 03/27/2023] [Indexed: 04/29/2023]
Abstract
Type VI CRISPR-Cas systems use RNA-guided ribonuclease (RNase) Cas13 to defend bacteria against viruses, and some of these systems encode putative membrane proteins that have unclear roles in Cas13-mediated defense. We show that Csx28, of type VI-B2 systems, is a transmembrane protein that assists to slow cellular metabolism upon viral infection, increasing antiviral defense. High-resolution cryo-electron microscopy reveals that Csx28 forms an octameric pore-like structure. These Csx28 pores localize to the inner membrane in vivo. Csx28's antiviral activity in vivo requires sequence-specific cleavage of viral messenger RNAs by Cas13b, which subsequently results in membrane depolarization, slowed metabolism, and inhibition of sustained viral infection. Our work suggests a mechanism by which Csx28 acts as a downstream, Cas13b-dependent effector protein that uses membrane perturbation as an antiviral defense strategy.
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Affiliation(s)
- Arica R. VanderWal
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester; Rochester, USA
- Center for RNA Biology, University of Rochester; Rochester, USA
| | - Jung-Un Park
- Department of Molecular Biology and Genetics, Cornell University; Ithaca, USA
| | - Bogdan Polevoda
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester; Rochester, USA
- Center for RNA Biology, University of Rochester; Rochester, USA
| | - Julia K. Nicosia
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester; Rochester, USA
- Center for RNA Biology, University of Rochester; Rochester, USA
| | - Adrian M. Molina Vargas
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester; Rochester, USA
- Center for RNA Biology, University of Rochester; Rochester, USA
| | | | - Mitchell R. O’Connell
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester; Rochester, USA
- Center for RNA Biology, University of Rochester; Rochester, USA
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Kang N, Thuy LT, Dongquoc V, Choi JS. Conjugation of Short Oligopeptides to a Second-Generation Polyamidoamine Dendrimer Shows Antibacterial Activity. Pharmaceutics 2023; 15:pharmaceutics15031005. [PMID: 36986864 PMCID: PMC10053621 DOI: 10.3390/pharmaceutics15031005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 03/15/2023] [Accepted: 03/19/2023] [Indexed: 03/30/2023] Open
Abstract
The growing evolution of bacterial resistance to antibiotics represents a global issue that not only impacts healthcare systems but also political and economic processes. This necessitates the development of novel antibacterial agents. Antimicrobial peptides have shown promise in this regard. Thus, in this study, a new functional polymer was synthesized by joining a short oligopeptide sequence (Phe-Lys-Phe-Leu, FKFL) to the surface of a second-generation polyamidoamine (G2 PAMAM) dendrimer as an antibacterial component. This method of synthesis proved simple and resulted in a high conjugation yield of the product FKFL-G2. To determine its antibacterial potential, FKFL-G2 was subsequently analyzed via mass spectrometry, a cytotoxicity assay, bacterial growth assay, colony-forming unit assay, membrane permeabilization assay, transmission electron microscopy, and biofilm formation assay. FKFL-G2 was found to exhibit low toxicity to noncancerous NIH3T3 cells. Additionally, FKFL-G2 had an antibacterial effect on Escherichia coli and Staphylococcus aureus strains by interacting with and disrupting the bacterial cell membrane. Based on these findings, FKFL-G2 shows promise as a potential antibacterial agent.
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Affiliation(s)
- Namyoung Kang
- Department of Biochemistry, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Republic of Korea
| | - Le Thi Thuy
- Department of Biochemistry, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Republic of Korea
| | - Viet Dongquoc
- Department of Materials Science and Engineering, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Republic of Korea
| | - Joon Sig Choi
- Department of Biochemistry, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Republic of Korea
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Butler D, Kammarchedu V, Zhou K, Peeke L, Lyle L, Snyder DW, Ebrahimi A. Cellulose-Based Laser-Induced Graphene Devices for Electrochemical Monitoring of Bacterial Phenazine Production and Viability. SENSORS AND ACTUATORS. B, CHEMICAL 2023; 378:133090. [PMID: 36644326 PMCID: PMC9835725 DOI: 10.1016/j.snb.2022.133090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
As an easily disposable substrate with a microporous texture, paper is a well-suited, generic substrate to build analytical devices for studying bacteria. Using a multi-pass lasing process, cellulose-based laser-induced graphene (cLIG) with a sheet resistance of 43.7 ± 2.3 Ωsq-1 is developed and utilized in the fabrication of low-cost and environmentally-friendly paper sensor arrays. Two case studies with Pseudomonas aeruginosa and Escherichia coli demonstrate the practicality of the cLIG sensors for the electrochemical analysis of bacteria. The first study measures the time-dependent profile of phenazines released from both planktonic (up to 60 h) and on-chip-grown (up to 22 h) Pseudomonas aeruginosa cultures. While similarities do exist, marked differences in phenazine production are seen with cells grown directly on cLIG compared to the planktonic culture. Moreover, in planktonic cultures, pyocyanin levels increase early on and plateau around 20 h, while optical density measurements increase monotonically over the duration of testing. The second study monitors the viability and metabolic activity of Escherichia coli using a resazurin-based electrochemical assay. These results demonstrate the utility of cLIG paper sensors as an inexpensive and versatile platform for monitoring bacteria and could enable new opportunities in high-throughput antibiotic susceptibility testing, ecological studies, and biofilm studies.
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Affiliation(s)
- Derrick Butler
- Department of Electrical Engineering, The Pennsylvania State University, University Park, PA 16802
- Center for Atomically Thin Multifunctional Coatings, The Pennsylvania State University, University Park, PA 16802
| | - Vinay Kammarchedu
- Department of Electrical Engineering, The Pennsylvania State University, University Park, PA 16802
- Center for Atomically Thin Multifunctional Coatings, The Pennsylvania State University, University Park, PA 16802
- Center for Biodevices, The Pennsylvania State University, University Park, PA 16802
| | - Keren Zhou
- Department of Electrical Engineering, The Pennsylvania State University, University Park, PA 16802
| | - Lachlan Peeke
- Applied Research Laboratory - Electronic Materials and Devices Department, The Pennsylvania State University, University Park, PA 16802
- Department of Materials Science and Engineering, The Pennsylvania State University, University Park, PA 16802
| | - Luke Lyle
- Applied Research Laboratory - Electronic Materials and Devices Department, The Pennsylvania State University, University Park, PA 16802
- Department of Materials Science and Engineering, The Pennsylvania State University, University Park, PA 16802
| | - David W Snyder
- Applied Research Laboratory - Electronic Materials and Devices Department, The Pennsylvania State University, University Park, PA 16802
- Department of Materials Science and Engineering, The Pennsylvania State University, University Park, PA 16802
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA 16802
| | - Aida Ebrahimi
- Department of Electrical Engineering, The Pennsylvania State University, University Park, PA 16802
- Center for Atomically Thin Multifunctional Coatings, The Pennsylvania State University, University Park, PA 16802
- Center for Biodevices, The Pennsylvania State University, University Park, PA 16802
- Department of Biomedical Engineering, The Pennsylvania State University, University Park, PA 16802
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21
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Heithoff DM, Mahan SP, Barnes V L, Leyn SA, George CX, Zlamal JE, Limwongyut J, Bazan GC, Fried JC, Fitzgibbons LN, House JK, Samuel CE, Osterman AL, Low DA, Mahan MJ. A broad-spectrum synthetic antibiotic that does not evoke bacterial resistance. EBioMedicine 2023; 89:104461. [PMID: 36801104 PMCID: PMC10025758 DOI: 10.1016/j.ebiom.2023.104461] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 01/17/2023] [Accepted: 01/18/2023] [Indexed: 02/17/2023] Open
Abstract
BACKGROUND Antimicrobial resistance (AMR) poses a critical threat to public health and disproportionately affects the health and well-being of persons in low-income and middle-income countries. Our aim was to identify synthetic antimicrobials termed conjugated oligoelectrolytes (COEs) that effectively treated AMR infections and whose structures could be readily modified to address current and anticipated patient needs. METHODS Fifteen chemical variants were synthesized that contain specific alterations to the COE modular structure, and each variant was evaluated for broad-spectrum antibacterial activity and for in vitro cytotoxicity in cultured mammalian cells. Antibiotic efficacy was analyzed in murine models of sepsis; in vivo toxicity was evaluated via a blinded study of mouse clinical signs as an outcome of drug treatment. FINDINGS We identified a compound, COE2-2hexyl, that displayed broad-spectrum antibacterial activity. This compound cured mice infected with clinical bacterial isolates derived from patients with refractory bacteremia and did not evoke bacterial resistance. COE2-2hexyl has specific effects on multiple membrane-associated functions (e.g., septation, motility, ATP synthesis, respiration, membrane permeability to small molecules) that may act together to negate bacterial cell viability and the evolution of drug-resistance. Disruption of these bacterial properties may occur through alteration of critical protein-protein or protein-lipid membrane interfaces-a mechanism of action distinct from many membrane disrupting antimicrobials or detergents that destabilize membranes to induce bacterial cell lysis. INTERPRETATION The ease of molecular design, synthesis and modular nature of COEs offer many advantages over conventional antimicrobials, making synthesis simple, scalable and affordable. These COE features enable the construction of a spectrum of compounds with the potential for development as a new versatile therapy for an imminent global health crisis. FUNDING U.S. Army Research Office, National Institute of Allergy and Infectious Diseases, and National Heart, Lung, and Blood Institute.
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Affiliation(s)
- Douglas M Heithoff
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA, 93106, USA; Institute for Collaborative Biotechnologies, University of California, Santa Barbara, CA, 93106, USA
| | - Scott P Mahan
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA, 93106, USA; Institute for Collaborative Biotechnologies, University of California, Santa Barbara, CA, 93106, USA; Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, CA, 95616, USA
| | - Lucien Barnes V
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA, 93106, USA; Institute for Collaborative Biotechnologies, University of California, Santa Barbara, CA, 93106, USA
| | - Semen A Leyn
- Infectious and Inflammatory Diseases Research Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, 92037, USA
| | - Cyril X George
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA, 93106, USA; Institute for Collaborative Biotechnologies, University of California, Santa Barbara, CA, 93106, USA
| | - Jaime E Zlamal
- Infectious and Inflammatory Diseases Research Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, 92037, USA
| | - Jakkarin Limwongyut
- Institute for Collaborative Biotechnologies, University of California, Santa Barbara, CA, 93106, USA; Center for Polymers and Organic Solids, Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA, 93106, USA
| | - Guillermo C Bazan
- Institute for Collaborative Biotechnologies, University of California, Santa Barbara, CA, 93106, USA; Center for Polymers and Organic Solids, Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA, 93106, USA; Department of Chemistry, National University of Singapore, 117543, Singapore
| | - Jeffrey C Fried
- Department of Medical Education, Santa Barbara Cottage Hospital, Santa Barbara, CA, 93105, USA; Department of Pulmonary and Critical Care Medicine, Santa Barbara Cottage Hospital, Santa Barbara, CA, 93105, USA
| | - Lynn N Fitzgibbons
- Department of Medical Education, Santa Barbara Cottage Hospital, Santa Barbara, CA, 93105, USA; Division of Infectious Diseases, Santa Barbara Cottage Hospital, Santa Barbara, CA, 93105, USA
| | - John K House
- Faculty of Science, Sydney School of Veterinary Science, The University of Sydney, Camden, New South Wales, 2570, Australia
| | - Charles E Samuel
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA, 93106, USA; Institute for Collaborative Biotechnologies, University of California, Santa Barbara, CA, 93106, USA
| | - Andrei L Osterman
- Infectious and Inflammatory Diseases Research Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, 92037, USA
| | - David A Low
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA, 93106, USA; Institute for Collaborative Biotechnologies, University of California, Santa Barbara, CA, 93106, USA.
| | - Michael J Mahan
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA, 93106, USA; Institute for Collaborative Biotechnologies, University of California, Santa Barbara, CA, 93106, USA.
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22
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Chen CH, Liao YH, Muljadi M, Lu TT, Cheng CM. Potential Application of the WST-8-mPMS Assay for Rapid Viable Microorganism Detection. Pathogens 2023; 12:pathogens12020343. [PMID: 36839615 PMCID: PMC9966898 DOI: 10.3390/pathogens12020343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 02/13/2023] [Accepted: 02/16/2023] [Indexed: 02/22/2023] Open
Abstract
To ensure clean drinking water, viable pathogens in water must be rapidly and efficiently screened. The traditional culture or spread-plate process-the conventional standard for bacterial detection-is laborious, time-consuming, and unsuitable for rapid detection. Therefore, we developed a colorimetric assay for rapid microorganism detection using a metabolism-based approach. The reaction between a viable microorganism and the combination of 2-(2-methoxy-4-nitrophenyl)-3-(4-nitrophenyl)-5-(2,4-disulfophenyl)-2H-tetrazolium sodium salt (WST-8) and 1-methoxy-5-methylphenazinium methyl sulfate (mPMS) results in a color change. In combination with a microplate reader, WST-8-mPMS reactivity was leveraged to develop a colorimetric assay for the rapid detection of various bacteria. The detection limit of the WST-8-mPMS assay for both gram-negative and gram-positive bacteria was evaluated. This WST-8-mPMS assay can be used to perform colorimetrical semi-quantitative detection of various bacterial strains in buffers or culture media within 1 h without incubation before the reaction. The easy-to-use, robust, rapid, and sensitive nature of this novel assay demonstrates its potential for practical and medical use for microorganism detection.
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Affiliation(s)
- Cheng-Han Chen
- Department of Emergency Medicine, Taipei Veterans General Hospital, Taipei 11217, Taiwan
- Institute of Biomedical Engineering, National Tsing Hua University, Hsinchu 30013, Taiwan
- School of Medicine, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan
| | - Yu-Hsiang Liao
- Institute of Biomedical Engineering, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Michael Muljadi
- Institute of Biomedical Engineering, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Tsai-Te Lu
- Institute of Biomedical Engineering, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Chao-Min Cheng
- Institute of Biomedical Engineering, National Tsing Hua University, Hsinchu 30013, Taiwan
- Correspondence:
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23
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Wątroba M, Bednarczyk W, Szewczyk PK, Kawałko J, Mech K, Grünewald A, Unalan I, Taccardi N, Boelter G, Banzhaf M, Hain C, Bała P, Boccaccini AR. In vitro cytocompatibility and antibacterial studies on biodegradable Zn alloys supplemented by a critical assessment of direct contact cytotoxicity assay. J Biomed Mater Res B Appl Biomater 2023; 111:241-260. [PMID: 36054531 PMCID: PMC10086991 DOI: 10.1002/jbm.b.35147] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 07/11/2022] [Accepted: 07/17/2022] [Indexed: 12/15/2022]
Abstract
In vitro cytotoxicity assessment is indispensable in developing new biodegradable implant materials. Zn, which demonstrates an ideal corrosion rate between Mg- and Fe-based alloys, has been reported to have excellent in vivo biocompatibility. Therefore, modifications aimed at improving Zn's mechanical properties should not degrade its biological response. As sufficient strength, ductility and corrosion behavior required of load-bearing implants has been obtained in plastically deformed Zn-3Ag-0.5Mg, the effect of simultaneous Ag and Mg additions on in vitro cytocompatibility and antibacterial properties was studied, in relation to Zn and Zn-3Ag. Direct cell culture on samples and indirect extract-based tests showed almost no significant differences between the tested Zn-based materials. The diluted extracts of Zn, Zn-3Ag, and Zn-3Ag-0.5Mg showed no cytotoxicity toward MG-63 cells at a concentration of ≤12.5%. The cytotoxic effect was observed only at high Zn2+ ion concentrations and when in direct contact with metallic samples. The highest LD50 (lethal dose killing 50% of cells) of 13.4 mg/L of Zn2+ ions were determined for the Zn-3Ag-0.5Mg. Similar antibacterial activity against Escherichia coli and Staphylococcus aureus was observed for Zn and Zn alloys, so the effect is attributed mainly to the released Zn2+ ions exhibiting bactericidal properties. Most importantly, our experiments indicated the limitations of water-soluble tetrazolium salt-based cytotoxicity assays for direct tests on Zn-based materials. The discrepancies between the WST-8 assay and SEM observations are attributed to the interference of Zn2+ ions with tetrazolium salt, therefore favoring its transformation into formazan, giving false cell viability quantitative results.
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Affiliation(s)
- Maria Wątroba
- Laboratory for Mechanics of Materials and Nanostructures, Empa, Swiss Federal Laboratories for Materials Science and Technology, Thun, Switzerland.,Faculty of Metals Engineering and Industrial Computer Science, AGH University of Science and Technology, Krakow, Poland
| | - Wiktor Bednarczyk
- Faculty of Materials Science and Engineering, Warsaw University of Technology, Warsaw, Poland
| | - Piotr K Szewczyk
- Faculty of Metals Engineering and Industrial Computer Science, AGH University of Science and Technology, Krakow, Poland
| | - Jakub Kawałko
- Academic Centre for Materials and Nanotechnology, AGH University of Science and Technology, Krakow, Poland
| | - Krzysztof Mech
- Academic Centre for Materials and Nanotechnology, AGH University of Science and Technology, Krakow, Poland
| | - Alina Grünewald
- Department of Materials Science and Engineering, Institute of Biomaterials, University of Erlangen-Nuremberg, Erlangen, Germany
| | - Irem Unalan
- Department of Materials Science and Engineering, Institute of Biomaterials, University of Erlangen-Nuremberg, Erlangen, Germany
| | - Nicola Taccardi
- Institute of Chemical Reaction Engineering, University of Erlangen-Nuremberg, Erlangen, Germany
| | - Gabriela Boelter
- Institute of Microbiology and Infection and School of Biosciences, University of Birmingham, Birmingham, UK
| | - Manuel Banzhaf
- Institute of Microbiology and Infection and School of Biosciences, University of Birmingham, Birmingham, UK
| | - Caroline Hain
- Laboratory for Mechanics of Materials and Nanostructures, Empa, Swiss Federal Laboratories for Materials Science and Technology, Thun, Switzerland.,Institute for Applied Laser Photonics and Surface Technologies ALPS, Bern University of Applied Sciences, Biel/Bienne, Switzerland
| | - Piotr Bała
- Faculty of Metals Engineering and Industrial Computer Science, AGH University of Science and Technology, Krakow, Poland.,Academic Centre for Materials and Nanotechnology, AGH University of Science and Technology, Krakow, Poland
| | - Aldo R Boccaccini
- Department of Materials Science and Engineering, Institute of Biomaterials, University of Erlangen-Nuremberg, Erlangen, Germany
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24
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Kulišová M, Maťátková O, Brányik T, Zelenka J, Drábová L, Kolouchová IJ. Detection of microscopic filamentous fungal biofilms - Choosing the suitable methodology. J Microbiol Methods 2023; 205:106676. [PMID: 36693497 DOI: 10.1016/j.mimet.2023.106676] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 01/18/2023] [Accepted: 01/18/2023] [Indexed: 01/22/2023]
Abstract
Microscopic filamentous fungi are ubiquitous microorganisms that adapt very easily to a variety of environmental conditions. Due to this adaptability, they can colonize a number of various surfaces where they are able to start forming biofilms. Life in the form of biofilms provides them with many benefits (increased resistance to desiccation, UV radiation, antimicrobial compounds, and host immune response). The aim of this study is to find a reliable and reproducible methodology to determine biofilm growth of selected microscopic filamentous fungi strains. Several methods (crystal violet staining, MTT assay, XTT assay, resazurin assay) for the determination of total biofilm biomass and its metabolic activity were tested on four fungi - Alternaria alternata, Aspergillus niger, Fusarium culmorum and Fusarium graminearum, and their biofilm was also imaged by spinning disc confocal microscopy using fluorescent dyes. A reproducible biofilm quantification method is essential for the subsequent testing of the biofilm growth suppression using antifungal agents or physical methods. Crystal violet staining was found to be a suitable method for the determination of total biofilm biomass of selected strains, and the MTT assay for the determination of metabolic activity of the biofilms. Calcofluor white and Nile red fluorescent stains successfully dyed the hyphae of microscopic fungi.
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Affiliation(s)
- Markéta Kulišová
- Department of Biotechnology, University of Chemistry and Technology, Prague, Technická 5, Prague 166 28, Czech Republic.
| | - Olga Maťátková
- Department of Biotechnology, University of Chemistry and Technology, Prague, Technická 5, Prague 166 28, Czech Republic.
| | - Tomáš Brányik
- Research Institute of Brewing and Malting, Lipová 511/15, Prague 120 44, Czech Republic.
| | - Jaroslav Zelenka
- Department of Biochemistry and Microbiology, University of Chemistry and Technology, Prague, Technická 5, Prague 166 28, Czech Republic.
| | - Lucie Drábová
- Department of Food Analysis and Nutrition, University of Chemistry and Technology, Prague, Technická 5, Prague 166 28, Czech Republic.
| | - Irena Jarošová Kolouchová
- Department of Biotechnology, University of Chemistry and Technology, Prague, Technická 5, Prague 166 28, Czech Republic.
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25
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Zamzami M, Alamoudi S, Ahmad A, Choudhry H, Khan MI, Hosawi S, Rabbani G, Shalaan ES, Arkook B. Direct Identification of Label-Free Gram-Negative Bacteria with Bioreceptor-Free Concentric Interdigitated Electrodes. BIOSENSORS 2023; 13:179. [PMID: 36831945 PMCID: PMC9953431 DOI: 10.3390/bios13020179] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 01/05/2023] [Accepted: 01/17/2023] [Indexed: 06/18/2023]
Abstract
This investigation demonstrates an electrochemical method for directly identifying unlabeled Gram-negative bacteria without other additives or labeling agents. After incubation, the bacterial cell surface is linked to the interdigitated electrode through electroadsorption. Next, these cells are exposed to a potential difference between the two electrodes. The design geometry of an electrode has a significant effect on the electrochemical detection of Gram-negative bacteria. Therefore, electrode design geometry is a crucial factor that needs to be considered when designing electrodes for electrochemical sensing. They provide the area for the reaction and are responsible for transferring electrons from one electrode to another. This work aims to study the available design in the commercial market to determine the most suitable electrode geometry with a high detection sensitivity that can be used to identify and quantify bacterial cells in normal saline solutions. To work on detecting bacterial cells without the biorecognition element, we have to consider the microelectrode's design, which makes it very susceptible to bacteria size. The concentration-dilution technique measures the effect of the concentration on label-free Gram-negative bacteria in a normal saline solution without needing bio-recognized elements for a fast screening evaluation. This method's limit of detection (LOD) cannot measure concentrations less than 102 CFU/mL and cannot distinguish between live and dead cells. Nevertheless, this approach exhibited excellent detection performance under optimal experimental conditions and took only a few hours.
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Affiliation(s)
- Mazin Zamzami
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
- Center for Artificial Intelligence in Precision Medicines, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Samer Alamoudi
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Abrar Ahmad
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Hani Choudhry
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
- Center for Artificial Intelligence in Precision Medicines, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Mohammad Imran Khan
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
- Center for Artificial Intelligence in Precision Medicines, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Salman Hosawi
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
- Center for Artificial Intelligence in Precision Medicines, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Gulam Rabbani
- Department of Medical Biotechnology, Yeungnam University, 280 Daehak-ro, Gyeongsan 38541, Gyeongbuk, Republic of Korea
| | - El-Sayed Shalaan
- Department of Physics, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Bassim Arkook
- Department of Physics, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
- Department of Physics and Astronomy, University of California, Riverside, CA 92521, USA
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26
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Jalandra R, Makharia GK, Sharma M, Kumar A. Inflammatory and deleterious role of gut microbiota-derived trimethylamine on colon cells. Front Immunol 2023; 13:1101429. [PMID: 36726978 PMCID: PMC9885123 DOI: 10.3389/fimmu.2022.1101429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 12/28/2022] [Indexed: 01/18/2023] Open
Abstract
Trimethylamine (TMA) is produced by the intestinal microbiota as a by-product of metabolism of dietary precursors. TMA has been implicated in various chronic health conditions. However, the effect of TMA in the colon and the underlying mechanism was not clear. In this study, TMA exhibited toxic effects in vitro as well as in vivo. TMA-induced oxidative stress causes DNA damage, and compromised cell membrane integrity leading to the release of LDH outside the cells which ultimately leads to cell death. Besides, TMA also exhibited pronounced increase in cell cycle arrest at G2/M phase in both HCT116 and HT29 cell lines. TMA was found to be genotoxic and cytotoxic as the TMA concentration increased from 0.15 mM. A decreased ATP intracellular content was observed after 24 h, 48 h, and 72 h treatment in a time and dose-dependent manner. For in vivo research, TMA (100 mM, i.p. and intra-rectal) once a week for 12 weeks caused significant changes in cellular morphology of colon and rectum epithelium as assessed by H & E staining. TMA also significantly increased the infiltration of inflammatory cells in the colon and rectal epithelium indicating the severity of inflammation. In addition, TMA caused extensive mucosal damage and distortion in the epithelium, decrease in length of small intestine compared to control mice. In conclusion, these results highlight the detrimental effects of TMA in the colon and rectal epithelium.
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Affiliation(s)
- Rekha Jalandra
- Gene Regulation Laboratory, National Institute of Immunology, New Delhi, India
- Department of Zoology, Maharshi Dayanand University, Rohtak, India
| | - Govind K. Makharia
- Department of Gastroenterology and Human Nutrition, All India Institute of Medical Sciences, New Delhi, India
| | - Minakshi Sharma
- Department of Zoology, Maharshi Dayanand University, Rohtak, India
| | - Anil Kumar
- Gene Regulation Laboratory, National Institute of Immunology, New Delhi, India
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27
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Shajib MS, Futrega K, Franco RAG, McKenna E, Guillesser B, Klein TJ, Crawford RW, Doran MR. Method for manufacture and cryopreservation of cartilage microtissues. J Tissue Eng 2023; 14:20417314231176901. [PMID: 37529249 PMCID: PMC10387698 DOI: 10.1177/20417314231176901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 05/04/2023] [Indexed: 08/03/2023] Open
Abstract
The financial viability of a cell and tissue-engineered therapy may depend on the compatibility of the therapy with mass production and cryopreservation. Herein, we developed a method for the mass production and cryopreservation of 3D cartilage microtissues. Cartilage microtissues were assembled from either 5000 human bone marrow-derived stromal cells (BMSC) or 5000 human articular chondrocytes (ACh) each using a customized microwell platform (the Microwell-mesh). Microtissues rapidly accumulate homogenous cartilage-like extracellular matrix (ECM), making them potentially useful building blocks for cartilage defect repair. Cartilage microtissues were cultured for 5 or 10 days and then cryopreserved in 90% serum plus 10% dimethylsulfoxide (DMSO) or commercial serum-free cryopreservation media. Cell viability was maximized during thawing by incremental dilution of serum to reduce oncotic shock, followed by washing and further culture in serum-free medium. When assessed with live/dead viability dyes, thawed microtissues demonstrated high viability but reduced immediate metabolic activity relative to unfrozen control microtissues. To further assess the functionality of the freeze-thawed microtissues, their capacity to amalgamate into a continuous tissue was assess over a 14 day culture. The amalgamation of microtissues cultured for 5 days was superior to those that had been cultured for 10 days. Critically, the capacity of cryopreserved microtissues to amalgamate into a continuous tissue in a subsequent 14-day culture was not compromised, suggesting that cryopreserved microtissues could amalgamate within a cartilage defect site. The quality ECM was superior when amalgamation was performed in a 2% O2 atmosphere than a 20% O2 atmosphere, suggesting that this process may benefit from the limited oxygen microenvironment within a joint. In summary, cryopreservation of cartilage microtissues is a viable option, and this manipulation can be performed without compromising tissue function.
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Affiliation(s)
- Md. Shafiullah Shajib
- School of Biomedical Science, Faculty of Health, Queensland University of Technology, Brisbane, QLD, Australia
- Centre for Biomedical Technologies, School of Mechanical, Medical, and Process Engineering, Faculty of Engineering, Queensland University of Technology, Brisbane, QLD, Australia
- Translational Research Institute, Brisbane, QLD, Australia
| | - Kathryn Futrega
- Centre for Biomedical Technologies, School of Mechanical, Medical, and Process Engineering, Faculty of Engineering, Queensland University of Technology, Brisbane, QLD, Australia
- Translational Research Institute, Brisbane, QLD, Australia
- National Institute of Dental and Craniofacial Research, National Institutes of Health, Department of Health and Human Services, Bethesda, MD, USA
| | - Rose Ann G Franco
- Centre for Biomedical Technologies, School of Mechanical, Medical, and Process Engineering, Faculty of Engineering, Queensland University of Technology, Brisbane, QLD, Australia
- Translational Research Institute, Brisbane, QLD, Australia
| | - Eamonn McKenna
- Centre for Biomedical Technologies, School of Mechanical, Medical, and Process Engineering, Faculty of Engineering, Queensland University of Technology, Brisbane, QLD, Australia
- Translational Research Institute, Brisbane, QLD, Australia
| | - Bianca Guillesser
- School of Biomedical Science, Faculty of Health, Queensland University of Technology, Brisbane, QLD, Australia
- Centre for Biomedical Technologies, School of Mechanical, Medical, and Process Engineering, Faculty of Engineering, Queensland University of Technology, Brisbane, QLD, Australia
- Translational Research Institute, Brisbane, QLD, Australia
| | - Travis J Klein
- Centre for Biomedical Technologies, School of Mechanical, Medical, and Process Engineering, Faculty of Engineering, Queensland University of Technology, Brisbane, QLD, Australia
| | - Ross W Crawford
- Centre for Biomedical Technologies, School of Mechanical, Medical, and Process Engineering, Faculty of Engineering, Queensland University of Technology, Brisbane, QLD, Australia
| | - Michael R Doran
- School of Biomedical Science, Faculty of Health, Queensland University of Technology, Brisbane, QLD, Australia
- Centre for Biomedical Technologies, School of Mechanical, Medical, and Process Engineering, Faculty of Engineering, Queensland University of Technology, Brisbane, QLD, Australia
- Translational Research Institute, Brisbane, QLD, Australia
- National Institute of Dental and Craniofacial Research, National Institutes of Health, Department of Health and Human Services, Bethesda, MD, USA
- Mater Research Institute – University of Queensland, Brisbane, QLD, Australia
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28
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Yaneva Z, Ivanova D, Nikolova N, Toneva M. Organic dyes in contemporary medicinal chemistry and biomedicine. I. From the chromophore to the bioimaging/bioassay agent. BIOTECHNOL BIOTEC EQ 2022. [DOI: 10.1080/13102818.2022.2039077] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Affiliation(s)
- Zvezdelina Yaneva
- Department of Pharmacology, Animal Physiology, Biochemistry and Chemistry, Faculty of Veterinary Medicine, Trakia University, Stara Zagora, Bulgaria
| | - Donika Ivanova
- Department of Pharmacology, Animal Physiology, Biochemistry and Chemistry, Faculty of Veterinary Medicine, Trakia University, Stara Zagora, Bulgaria
| | - Nevena Nikolova
- Ecology Unit, Department of Pharmacology, Animal Physiology, Biochemistry and Chemistry, Faculty of Veterinary Medicine, Trakia University, Stara Zagora, Bulgaria
| | - Monika Toneva
- Department of Pharmacology, Animal Physiology, Biochemistry and Chemistry, Faculty of Veterinary Medicine, Trakia University, Stara Zagora, Bulgaria
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29
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Rösner LS, Walter F, Ude C, John GT, Beutel S. Sensors and Techniques for On-Line Determination of Cell Viability in Bioprocess Monitoring. BIOENGINEERING (BASEL, SWITZERLAND) 2022; 9:bioengineering9120762. [PMID: 36550968 PMCID: PMC9774925 DOI: 10.3390/bioengineering9120762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 11/07/2022] [Accepted: 11/30/2022] [Indexed: 12/12/2022]
Abstract
In recent years, the bioprocessing industry has experienced significant growth and is increasingly emerging as an important economic sector. Here, efficient process management and constant control of cellular growth are essential. Good product quality and yield can only be guaranteed with high cell density and high viability. Whereas the on-line measurement of physical and chemical process parameters has been common practice for many years, the on-line determination of viability remains a challenge and few commercial on-line measurement methods have been developed to date for determining viability in industrial bioprocesses. Thus, numerous studies have recently been conducted to develop sensors for on-line viability estimation, especially in the field of optical spectroscopic sensors, which will be the focus of this review. Spectroscopic sensors are versatile, on-line and mostly non-invasive. Especially in combination with bioinformatic data analysis, they offer great potential for industrial application. Known as soft sensors, they usually enable simultaneous estimation of multiple biological variables besides viability to be obtained from the same set of measurement data. However, the majority of the presented sensors are still in the research stage, and only a few are already commercially available.
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Affiliation(s)
- Laura S. Rösner
- Institute for Technical Chemistry, Leibniz University of Hanover, 30167 Hannover, Germany
| | - Franziska Walter
- Institute for Technical Chemistry, Leibniz University of Hanover, 30167 Hannover, Germany
| | - Christian Ude
- Institute for Technical Chemistry, Leibniz University of Hanover, 30167 Hannover, Germany
| | - Gernot T. John
- PreSens Precision Sensing GmbH, Am BioPark 11, 93053 Regensburg, Germany
| | - Sascha Beutel
- Institute for Technical Chemistry, Leibniz University of Hanover, 30167 Hannover, Germany
- Correspondence:
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30
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Zhang B, Peng C, Lu J, Hu X, Ren L. Enhancing menaquinone-7 biosynthesis by adaptive evolution of Bacillus natto through chemical modulator. BIORESOUR BIOPROCESS 2022; 9:120. [PMID: 38647796 PMCID: PMC10992315 DOI: 10.1186/s40643-022-00609-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 11/01/2022] [Indexed: 11/24/2022] Open
Abstract
Menaquinone-7 (MK-7) is a kind of vitamin K2 playing an important role in the treatment and prevention of cardiovascular disease, osteoporosis and arterial calcification. The purpose of this study is to establish an adaptive evolution strategy based on a chemical modulator to improve MK-7 biosynthesis in Bacillus natto. The inhibitor of 5-enolpyruvylshikimate-3-phosphate synthase (EPSP synthase), glyphosate, was chosen as the chemical modulator to perform the experiments. The final strain ALE-25-40, which was obtained after 40 cycles in 25 mmol/L glyphosate, showed a maximal MK-7 titer of 62 mg/L and MK-7 productivity of 0.42 mg/(L h), representing 2.5 and 3 times the original strain, respectively. Moreover, ALE-25-40 generated fewer spores and showed a higher NADH and redox potential. Furthermore, the mechanism related to the improved performance of ALE-25-40 was investigated by comparative transcriptomics analysis. Genes related to the sporation formation were down-regulated. In addition, several genes related to NADH formation were also up-regulated. This strategy proposed here may provide a new and alternative directive for the industrial production of vitamin K2.
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Affiliation(s)
- Bei Zhang
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30 South Puzhu Road, Nanjing, 211816, People's Republic of China
| | - Cheng Peng
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30 South Puzhu Road, Nanjing, 211816, People's Republic of China
| | - Jianyao Lu
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30 South Puzhu Road, Nanjing, 211816, People's Republic of China
| | - Xuechao Hu
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30 South Puzhu Road, Nanjing, 211816, People's Republic of China
- Shanghai JanStar Technology Development Co., Ltd., No. 1288, Huateng Road, Shanghai, 201700, China
| | - Lujing Ren
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30 South Puzhu Road, Nanjing, 211816, People's Republic of China.
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31
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Dediu V, Busila M, Tucureanu V, Bucur FI, Iliescu FS, Brincoveanu O, Iliescu C. Synthesis of ZnO/Au Nanocomposite for Antibacterial Applications. NANOMATERIALS (BASEL, SWITZERLAND) 2022; 12:nano12213832. [PMID: 36364608 PMCID: PMC9655429 DOI: 10.3390/nano12213832] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 10/26/2022] [Accepted: 10/26/2022] [Indexed: 06/01/2023]
Abstract
Annually, antimicrobial-resistant infections-related mortality worldwide accelerates due to the increased use of antibiotics during the coronavirus pandemic and the antimicrobial resistance, which grows exponentially, and disproportionately to the current rate of development of new antibiotics. Nanoparticles can be an alternative to the current therapeutic approach against multi-drug resistance microorganisms caused infections. The motivation behind this work was to find a superior antibacterial nanomaterial, which can be efficient, biocompatible, and stable in time. This study evaluated the antibacterial activity of ZnO-based nanomaterials with different morphologies, synthesized through the solvothermal method and further modified with Au nanoparticles through wet chemical reduction. The structure, crystallinity, and morphology of ZnO and ZnO/Au nanomaterials have been investigated with XRD, SEM, TEM, DLS, and FTIR spectroscopy. The antibacterial effect of unmodified ZnO and ZnO/Au nanomaterials against Escherichia coli and Staphylococcus aureus was investigated through disc diffusion and tetrazolium/formazan (TTC) assays. The results showed that the proposed nanomaterials exhibited significant antibacterial effects on the Gram-positive and Gram-negative bacteria. Furthermore, ZnO nanorods with diameters smaller than 50 nm showed better antibacterial activity than ZnO nanorods with larger dimensions. The antibacterial efficiency against Escherichia coli and Staphylococcus aureus improved considerably by adding 0.2% (w/w) Au to ZnO nanorods. The results indicated the new materials' potential for antibacterial applications.
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Affiliation(s)
- Violeta Dediu
- National Research and Development Institute in Microtechnologies—IMT Bucharest, 126A Erou Iancu Nicolae Street, 077190 Bucharest, Romania
| | - Mariana Busila
- Centre of Nanostructures and Functional Materials-CNMF, “Dunarea de Jos” University of Galati, Domneasca Street 111, 800201 Galati, Romania
| | - Vasilica Tucureanu
- National Research and Development Institute in Microtechnologies—IMT Bucharest, 126A Erou Iancu Nicolae Street, 077190 Bucharest, Romania
| | - Florentina Ionela Bucur
- Faculty of Food Science and Engineering, “Dunarea de Jos University” of Galati, Domneasca Street 111, 800201 Galati, Romania
| | - Florina Silvia Iliescu
- National Research and Development Institute in Microtechnologies—IMT Bucharest, 126A Erou Iancu Nicolae Street, 077190 Bucharest, Romania
| | - Oana Brincoveanu
- National Research and Development Institute in Microtechnologies—IMT Bucharest, 126A Erou Iancu Nicolae Street, 077190 Bucharest, Romania
| | - Ciprian Iliescu
- National Research and Development Institute in Microtechnologies—IMT Bucharest, 126A Erou Iancu Nicolae Street, 077190 Bucharest, Romania
- Faculty of Chemical Engineering and Biotechnologies, University “Politehnica” of Bucharest, 011061 Bucharest, Romania
- Academy of Romanian Scientists, 010071 Bucharest, Romania
- Regional Institute of Oncology, Iasi TRANSCEND Research Center, 2-4 General Henri Mathias Berthelot, 700483 Iasi, Romania
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32
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Lichtenberg M, Kragh KN, Fritz B, Kirkegaard JB, Tolker-Nielsen T, Bjarnsholt T. Cyclic-di-GMP signaling controls metabolic activity in Pseudomonas aeruginosa. Cell Rep 2022; 41:111515. [DOI: 10.1016/j.celrep.2022.111515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 07/13/2022] [Accepted: 09/26/2022] [Indexed: 11/03/2022] Open
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Tien T, Saccomano SC, Martin PA, Armstrong MS, Prud’homme RK, Cash KJ. Sensors in a Flash! Oxygen Nanosensors for Microbial Metabolic Monitoring Synthesized by Flash Nanoprecipitation. ACS Sens 2022; 7:2606-2614. [PMID: 36053212 PMCID: PMC9513798 DOI: 10.1021/acssensors.2c00859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 08/25/2022] [Indexed: 01/31/2023]
Abstract
Flash nanoprecipitation (FNP) is an efficient and scalable nanoparticle synthesis method that has not previously been applied to nanosensor fabrication. Current nanosensor fabrication methods have traditionally exhibited poor replicability and consistency resulting in high batch-to-batch variability, highlighting the need for a more tunable and efficient method such as FNP. We used FNP to fabricate nanosensors to sense oxygen based on an oxygen-sensitive dye and a reference dye, as a tool for measuring microbial metabolism. We used fluorescence spectroscopy to optimize nanosensor formulations, calibrate the nanosensors for oxygen concentration determination, and measure oxygen concentrations through oxygen-sensitive dye luminescence. FNP provides an effective platform for making sensors capable of responding to oxygen concentration in gas-bubbled solutions as well as in microbial environments. The environments we tested the sensors in arePseudomonas aeruginosa biofilms andSaccharomyces cerevisiae liquid cultures─both settings where oxygen concentration is highly dependent on microbial activity. With FNP now applied to nanosensor fabrication, future nanosensor applications can take advantage of improved product quality through better replicability and consistency while maintaining the original function of the nanosensor.
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Affiliation(s)
- Tony Tien
- Chemical
and Biological Engineering, Colorado School
of Mines, Golden, Colorado 80401, United States
| | - Samuel C. Saccomano
- Chemical
and Biological Engineering, Colorado School
of Mines, Golden, Colorado 80401, United States
| | - Pilar A. Martin
- Chemical
and Biological Engineering, Colorado School
of Mines, Golden, Colorado 80401, United States
| | - Madeleine S. Armstrong
- Chemical
and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - Robert K. Prud’homme
- Chemical
and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - Kevin J. Cash
- Chemical
and Biological Engineering, Colorado School
of Mines, Golden, Colorado 80401, United States
- Quantitative
Biosciences and Engineering, Colorado School
of Mines, Golden, Colorado 80401, United
States
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34
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Daubie V, Chalhoub H, Blasdel B, Dahma H, Merabishvili M, Glonti T, De Vos N, Quintens J, Pirnay JP, Hallin M, Vandenberg O. Determination of phage susceptibility as a clinical diagnostic tool: A routine perspective. Front Cell Infect Microbiol 2022; 12:1000721. [PMID: 36211951 PMCID: PMC9532704 DOI: 10.3389/fcimb.2022.1000721] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 08/30/2022] [Indexed: 11/13/2022] Open
Abstract
As the global burden of disease caused by multidrug resistant bacteria is a major source of concern, credible clinical alternatives to antibiotic therapy, such as personalized phage therapy, are actively explored. Although phage therapy has been used for more than a century, the issue of an easy to implement diagnostic tool for determining phage susceptibility that meets current routine clinical needs is still open. In this Review, we summarize the existing methods used for determining phage activity on bacteria, including the three reference methods: the spot test, the double agar overlay plaque assay, and the Appelmans method. The first two methods rely on the principle of challenging the overnight growth of a lawn of bacteria in an agar matrix to a known relative phage to bacteria concentration and represent good screening tools to determine if the tested phage can be used for a “passive” and or “active” treatment. Beside these methods, several techniques, based on “real-time” growth kinetics assays (GKA) have been developed or are under development. They all monitor the growth of clinical isolates in the presence of phages, but use various detection methods, from classical optical density to more sophisticated techniques such as computer-assisted imagery, flow-cytometry, quantitative real-time polymerase chain reaction (qPCR) or metabolic indicators. Practical considerations as well as information provided about phage activity are reviewed for each technique. Finally, we also discuss the analytical and interpretative requirements for the implementation of a phage susceptibility testing tool in routine clinical microbiology.
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Affiliation(s)
- Valéry Daubie
- Innovation and Business Development Unit, LHUB-ULB, Université Libre de Bruxelles, Brussels, Belgium
- Department of Microbiology, LHUB-ULB, Université Libre de Bruxelles, Brussels, Belgium
| | - Houssein Chalhoub
- Innovation and Business Development Unit, LHUB-ULB, Université Libre de Bruxelles, Brussels, Belgium
- Centre for Environmental Health and Occupational Health, School of Public Health, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Bob Blasdel
- R&D department, Vesale Bioscience, Noville-sur-Mehaigne, Belgium
| | - Hafid Dahma
- Department of Microbiology, LHUB-ULB, Université Libre de Bruxelles, Brussels, Belgium
| | - Maya Merabishvili
- Laboratory for Molecular and Cellular Technology, Queen Astrid Military Hospital, Brussels, Belgium
| | - Tea Glonti
- Laboratory for Molecular and Cellular Technology, Queen Astrid Military Hospital, Brussels, Belgium
| | - Nathalie De Vos
- Department of Clinical Chemistry, LHUB-ULB, Université Libre de Bruxelles, Brussels, Belgium
| | - Johan Quintens
- R&D department, Vesale Bioscience, Noville-sur-Mehaigne, Belgium
| | - Jean-Paul Pirnay
- Laboratory for Molecular and Cellular Technology, Queen Astrid Military Hospital, Brussels, Belgium
| | - Marie Hallin
- Centre for Environmental Health and Occupational Health, School of Public Health, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Olivier Vandenberg
- Innovation and Business Development Unit, LHUB-ULB, Université Libre de Bruxelles, Brussels, Belgium
- Centre for Environmental Health and Occupational Health, School of Public Health, Université Libre de Bruxelles (ULB), Brussels, Belgium
- Division of Infection and Immunity, Faculty of Medical Sciences, University College London, London, United Kingdom
- *Correspondence: Olivier Vandenberg,
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35
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Trinh KTL, Lee NY. Recent Methods for the Viability Assessment of Bacterial Pathogens: Advances, Challenges, and Future Perspectives. Pathogens 2022; 11:pathogens11091057. [PMID: 36145489 PMCID: PMC9500772 DOI: 10.3390/pathogens11091057] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 09/14/2022] [Accepted: 09/15/2022] [Indexed: 11/28/2022] Open
Abstract
Viability assessment is a critical step in evaluating bacterial pathogens to determine infectious risks to public health. Based on three accepted viable criteria (culturability, metabolic activity, and membrane integrity), current viability assessments are categorized into three main strategies. The first strategy relies on the culturability of bacteria. The major limitation of this strategy is that it cannot detect viable but nonculturable (VBNC) bacteria. As the second strategy, based on the metabolic activity of bacteria, VBNC bacteria can be detected. However, VBNC bacteria sometimes can enter a dormant state that allows them to silence reproduction and metabolism; therefore, they cannot be detected based on culturability and metabolic activity. In order to overcome this drawback, viability assessments based on membrane integrity (third strategy) have been developed. However, these techniques generally require multiple steps, bulky machines, and laboratory technicians to conduct the tests, making them less attractive and popular applications. With significant advances in microfluidic technology, these limitations of current technologies for viability assessment can be improved. This review summarized and discussed the advances, challenges, and future perspectives of current methods for the viability assessment of bacterial pathogens.
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Affiliation(s)
- Kieu The Loan Trinh
- Department of Industrial Environmental Engineering, Gachon University, 1342 Seongnam-daero, Sujeong-gu, Seongnam-si 13120, Korea
| | - Nae Yoon Lee
- Department of BioNano Technology, Gachon University, 1342 Seongnam-daero, Sujeong-gu, Seongnam-si 13120, Korea
- Correspondence:
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36
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Duteil T, Bourillot R, Braissant O, Grégoire B, Leloup M, Portier E, Brigaud B, Féniès H, Svahn I, Henry A, Yokoyama Y, Visscher PT. Preservation of exopolymeric substances in estuarine sediments. Front Microbiol 2022; 13:921154. [PMID: 36060749 PMCID: PMC9434125 DOI: 10.3389/fmicb.2022.921154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 07/29/2022] [Indexed: 11/23/2022] Open
Abstract
The surface of intertidal estuarine sediments is covered with diatom biofilms excreting exopolymeric substances (EPSs) through photosynthesis. These EPSs are highly reactive and increase sediment cohesiveness notably through organo-mineral interactions. In most sedimentary environments, EPSs are partly to fully degraded by heterotrophic bacteria in the uppermost millimeters of the sediment and so they are thought to be virtually absent deeper in the sedimentary column. Here, we present the first evidence of the preservation of EPSs and EPS-mineral aggregates in a 6-m-long sedimentary core obtained from an estuarine point bar in the Gironde Estuary. EPSs were extracted from 18 depth intervals along the core, and their physicochemical properties were characterized by (i) wet chemical assays to measure the concentrations of polysaccharides and proteins, and EPS deprotonation of functional groups, (ii) acid–base titrations, and (iii) Fourier transform infrared spectroscopy. EPS-sediment complexes were also imaged using cryo-scanning electron microscopy. EPS results were analyzed in the context of sediment properties including facies, grain size, and total organic carbon, and of metabolic and enzymatic activities. Our results showed a predictable decrease in EPS concentrations (proteins and polysaccharides) and reactivity from the surface biofilm to a depth of 0.5 m, possibly linked to heterotrophic degradation. Concentrations remained relatively low down to ca. 4.3 m deep. Surprisingly, at that depth EPSs abundance was comparable to the surface and showed a downward decrease to 6.08 m. cryo-scanning electron microscopy (Cryo-SEM) showed that the EPS complexes with sediment were abundant at all studied depth and potentially protected EPSs from degradation. EPS composition did not change substantially from the surface to the bottom of the core. EPS concentrations and acidity were anti-correlated with metabolic activity, but showed no statistical correlation with grain size, TOC, depth or enzymatic activity. Maximum EPS concentrations were found at the top of tide-dominated sedimentary sequences, and very low concentrations were found in river flood-dominated sedimentary sequences. Based on this observation, we propose a scenario where biofilm development and EPS production are maximal when (i) the point bar and the intertidal areas were the most extensive, i.e., tide-dominated sequences and (ii) the tide-dominated deposit were succeeded by rapid burial beneath sediments, potentially decreasing the probability of encounter between bacterial cells and EPSs.
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Affiliation(s)
- Thibault Duteil
- Univ. Bordeaux, CNRS, Bordeaux INP, EPOC, UMR 5805, Pessac, France
- *Correspondence: Thibault Duteil,
| | | | - Olivier Braissant
- Department Biomedical Engineering (DBE), Center for Biomechanics and Biocalorimetry, University of Basel, Allschwil, Switzerland
| | - Brian Grégoire
- Institut de Chimie des Milieux et Matériaux de Poitiers (IC2MP), Centre National de la Recherche Scientifique (CNRS), Université de Poitiers, Poitiers, France
| | - Maud Leloup
- Institut de Chimie des Milieux et Matériaux de Poitiers (IC2MP), Centre National de la Recherche Scientifique (CNRS), Université de Poitiers, Poitiers, France
| | | | | | - Hugues Féniès
- Univ. Bordeaux, CNRS, Bordeaux INP, EPOC, UMR 5805, Pessac, France
| | - Isabelle Svahn
- Bordeaux Imaging Center (BIC), CNRS, Université de Bordeaux, Bordeaux, France
| | - Adrien Henry
- Univ. Bordeaux, CNRS, Bordeaux INP, EPOC, UMR 5805, Pessac, France
| | - Yusuke Yokoyama
- Department of Earth and Planetary Sciences, Atmosphere and Ocean Research Institute, University of Tokyo, Kashiwanoha, Chiba, Japan
| | - Pieter T. Visscher
- Department of Marine Sciences and Geosciences, University of Connecticut, Groton, CT, United States
- CNRS, Biogéosciences, Université de Bourgogne Franche-Comté, Dijon, France
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37
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Bioluminescent test systems based on firefly luciferase for studying stress effects on living cells. Biophys Rev 2022; 14:887-892. [PMID: 36124280 PMCID: PMC9481846 DOI: 10.1007/s12551-022-00978-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 06/30/2022] [Indexed: 12/13/2022] Open
Abstract
The bioluminescent luciferin-luciferase reaction is based on the oxidation of D-luciferin by oxygen in the presence of ATP and magnesium ions, catalyzed by firefly luciferase. The possibilities of using this reaction to study the influence of external effectors of a physical and chemical nature (temperature exposure, additions of drugs, membrane-active compounds, etc.) on living cells (prokaryotes and eukaryotes) are considered. Examples of the use of test systems based on living cells producing thermostable firefly luciferase for monitoring cellular homeostasis are given. The study of the kinetics of changes in the concentration of ATP and luciferase inside and outside cells made it possible to determine in dynamics the metabolic activity, cytotoxicity, and survival of cells under conditions of cellular stress, to study the processes of ATP synthesis/hydrolysis, and to evaluate the effectiveness of lytic agents in changing the permeability of the cell membrane.
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38
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Schleker ASS, Rist M, Matera C, Damijonaitis A, Collienne U, Matsuoka K, Habash SS, Twelker K, Gutbrod O, Saalwächter C, Windau M, Matthiesen S, Stefanovska T, Scharwey M, Marx MT, Geibel S, Grundler FMW. Mode of action of fluopyram in plant-parasitic nematodes. Sci Rep 2022; 12:11954. [PMID: 35831379 PMCID: PMC9279378 DOI: 10.1038/s41598-022-15782-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 06/29/2022] [Indexed: 11/10/2022] Open
Abstract
Plant-parasitic nematodes (PPN) are responsible for severe yield losses in crop production. Management is challenging as effective and safe means are rare. Recently, it has been discovered that the succinate dehydrogenase (SDH) inhibitor fluopyram is highly effective against PPN while accompanying an excellent safety profile. Here we show that fluopyram is a potent inhibitor of SDH in nematodes but not in mammals, insects and earthworm, explaining the selectivity on molecular level. As a consequence of SDH inhibition, fluopyram impairs ATP generation and causes paralysis in PPN and Caenorhabditis elegans. Interestingly, efficacy differences of fluopyram amongst PPN species can be observed. Permanent exposure to micromolar to nanomolar amounts of fluopyram prevents Meloidogyne spp. and Heterodera schachtii infection and their development at the root. Preincubation of Meloidogyne incognita J2 with fluopyram followed by a recovery period effectively reduces gall formation. However, the same procedure does not inhibit H. schachtii infection and development. Sequence comparison of sites relevant for ligand binding identified amino acid differences in SDHC which likely mediate selectivity, coincidently revealing a unique amino acid difference within SDHC conserved among Heterodera spp. Docking and C. elegans mutant studies suggest that this minute difference mediates altered sensitivity of H. schachtii towards fluopyram.
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Affiliation(s)
- A Sylvia S Schleker
- Molecular Phytomedicine, University of Bonn, Karlrobert-Kreiten-Straße 13, 53115, Bonn, Germany.
| | - Marc Rist
- Research and Development, CropScience Division, Bayer AG, Alfred-Nobel-Str.50, 40789, Monheim am Rhein, Germany.
| | - Christiane Matera
- Molecular Phytomedicine, University of Bonn, Karlrobert-Kreiten-Straße 13, 53115, Bonn, Germany
| | - Arunas Damijonaitis
- Research and Development, CropScience Division, Bayer AG, Alfred-Nobel-Str.50, 40789, Monheim am Rhein, Germany
| | - Ursel Collienne
- Research and Development, CropScience Division, Bayer AG, Alfred-Nobel-Str.50, 40789, Monheim am Rhein, Germany
| | - Koichi Matsuoka
- Molecular Phytomedicine, University of Bonn, Karlrobert-Kreiten-Straße 13, 53115, Bonn, Germany
| | - Samer S Habash
- Molecular Phytomedicine, University of Bonn, Karlrobert-Kreiten-Straße 13, 53115, Bonn, Germany
- BASF Vegetable Seeds, Napoleonsweg 152, 6083 AB, Nunhem, The Netherlands
| | - Katja Twelker
- Research and Development, CropScience Division, Bayer AG, Alfred-Nobel-Str.50, 40789, Monheim am Rhein, Germany
| | - Oliver Gutbrod
- Research and Development, CropScience Division, Bayer AG, Alfred-Nobel-Str.50, 40789, Monheim am Rhein, Germany
| | - Corinna Saalwächter
- Research and Development, CropScience Division, Bayer AG, Alfred-Nobel-Str.50, 40789, Monheim am Rhein, Germany
| | - Maren Windau
- Research and Development, CropScience Division, Bayer AG, Alfred-Nobel-Str.50, 40789, Monheim am Rhein, Germany
| | - Svend Matthiesen
- Research and Development, CropScience Division, Bayer AG, Alfred-Nobel-Str.50, 40789, Monheim am Rhein, Germany
| | - Tatyana Stefanovska
- Department of Entomology, National University of Life and Environmental Sciences, Kyiv, 03041, Ukraine
| | - Melanie Scharwey
- Research and Development, CropScience Division, Bayer AG, Alfred-Nobel-Str.50, 40789, Monheim am Rhein, Germany
| | - Michael T Marx
- Research and Development, CropScience Division, Bayer AG, Alfred-Nobel-Str.50, 40789, Monheim am Rhein, Germany
| | - Sven Geibel
- Research and Development, CropScience Division, Bayer AG, Alfred-Nobel-Str.50, 40789, Monheim am Rhein, Germany
| | - Florian M W Grundler
- Molecular Phytomedicine, University of Bonn, Karlrobert-Kreiten-Straße 13, 53115, Bonn, Germany
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Borah R, Das JM, Upadhyay J. Surface Functionalized Polyaniline Nanofibers:Chitosan Nanocomposite for Promoting Neuronal-like Differentiation of Primary Adipose Derived Mesenchymal Stem Cells and Urease Activity. ACS APPLIED BIO MATERIALS 2022; 5:3193-3211. [PMID: 35775198 DOI: 10.1021/acsabm.2c00171] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Bioscaffolds having electrically conducting polymers (CPs) have become increasingly relevant in tissue engineering (TE) because of their ability to regulate conductivity and promote biological function. With this in mind, the current study shows a conducting polyaniline nanofibers (PNFs) dispersed chitosan (Ch) nanocomposites scaffold with a simple one-step surface functionalization approach using glutaraldehyde for potential neural regeneration applications. According to the findings, 4 wt % PNFs dispersion in Ch matrix is an optimal concentration for achieving desirable biological functions while maintaining required physicochemical properties as evidenced by SEM, XRD, current-voltage (I-V) measurement, mechanical strength test, and in vitro biodegradability test. Surface chemical compositional analysis using XPS and ATR FT-IR confirms the incorporation of aldehyde functionality after functionalization, which is corroborated by surface energy calculations following the Van Oss-Chaudhury-Good method. Surface functionalization induced enhancement in surface hydrophilicity in terms of the polar component of surface energy (γiAB) from 6.35 to 12.54 mN m-1 along with an increase in surface polarity from 13.61 to 22.54%. Functionalized PNF:Ch scaffolds demonstrated improvement in enzyme activity from 67 to 94% and better enzyme kinetics with a reduction of Michaelis constants (Km) from 21.55 to 13.81 mM, indicating favorable protein-biomaterial interactions and establishing them as biologically perceptible materials. Surface functionalization mediated improved cell-biomaterial interactions led to improved viability, adhesion, and spreading of primary adipose derived mesenchymal stem cells (ADMSCs) as well as improved immunocompatibility. Cytoskeletal architecture assessment under differentiating media containing 10 ng/mL of each basic fibroblast growth factor (bFGF) and epidermal growth factor (EGF) revealed significant actin remodeling with neurite-like projections on the functionalized scaffolds after 14 days. Immunocytochemistry results showed that more than 85% of cells expressed early neuron specific β III tubulin protein on the functionalized scaffolds, whereas glial fibrillary acidic protein (GFAP) expression was limited to approximately 40% of cells. The findings point to the functionalized nanocomposites' potential as a smart scaffold for electrically stimulated neural regeneration, as they are flexible enough to be designed into microchanneled or conduit-like structures that mimic the microstructures and mechanical properties of peripheral nerves.
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Affiliation(s)
- Rajiv Borah
- Seri-Biotechnology Laboratory, Life Sciences Division, Institute of Advanced Study in Science & Technology, Guwahati 781035, India
| | - Jitu Mani Das
- Seri-Biotechnology Laboratory, Life Sciences Division, Institute of Advanced Study in Science & Technology, Guwahati 781035, India
| | - Jnanendra Upadhyay
- Department of Physics, Dakshin Kamrup College, Kamrup, Assam 781125, India
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40
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Al-madani H, Du H, Yao J, Peng H, Yao C, Jiang B, Wu A, Yang F. Living Sample Viability Measurement Methods from Traditional Assays to Nanomotion. BIOSENSORS 2022; 12:453. [PMID: 35884256 PMCID: PMC9313330 DOI: 10.3390/bios12070453] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 06/20/2022] [Accepted: 06/22/2022] [Indexed: 12/18/2022]
Abstract
Living sample viability measurement is an extremely common process in medical, pharmaceutical, and biological fields, especially drug pharmacology and toxicology detection. Nowadays, there are a number of chemical, optical, and mechanical methods that have been developed in response to the growing demand for simple, rapid, accurate, and reliable real-time living sample viability assessment. In parallel, the development trend of viability measurement methods (VMMs) has increasingly shifted from traditional assays towards the innovative atomic force microscope (AFM) oscillating sensor method (referred to as nanomotion), which takes advantage of the adhesion of living samples to an oscillating surface. Herein, we provide a comprehensive review of the common VMMs, laying emphasis on their benefits and drawbacks, as well as evaluating the potential utility of VMMs. In addition, we discuss the nanomotion technique, focusing on its applications, sample attachment protocols, and result display methods. Furthermore, the challenges and future perspectives on nanomotion are commented on, mainly emphasizing scientific restrictions and development orientations.
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Affiliation(s)
- Hamzah Al-madani
- Cixi Institute of Biomedical Engineering, International Cooperation Base of Biomedical Materials Technology and Application, Chinese Academy of Sciences (CAS), Key Laboratory of Magnetic Materials and Devices, Zhejiang Engineering Research Center for Biomedical Materials, Ningbo Institute of Materials Technology and Engineering, CAS, Ningbo 315201, China; (H.A.-m.); (H.D.); (J.Y.); (H.P.); (C.Y.); (B.J.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hui Du
- Cixi Institute of Biomedical Engineering, International Cooperation Base of Biomedical Materials Technology and Application, Chinese Academy of Sciences (CAS), Key Laboratory of Magnetic Materials and Devices, Zhejiang Engineering Research Center for Biomedical Materials, Ningbo Institute of Materials Technology and Engineering, CAS, Ningbo 315201, China; (H.A.-m.); (H.D.); (J.Y.); (H.P.); (C.Y.); (B.J.)
- College of Materials Sciences and Opto-Electronic Technology, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Junlie Yao
- Cixi Institute of Biomedical Engineering, International Cooperation Base of Biomedical Materials Technology and Application, Chinese Academy of Sciences (CAS), Key Laboratory of Magnetic Materials and Devices, Zhejiang Engineering Research Center for Biomedical Materials, Ningbo Institute of Materials Technology and Engineering, CAS, Ningbo 315201, China; (H.A.-m.); (H.D.); (J.Y.); (H.P.); (C.Y.); (B.J.)
- College of Materials Sciences and Opto-Electronic Technology, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hao Peng
- Cixi Institute of Biomedical Engineering, International Cooperation Base of Biomedical Materials Technology and Application, Chinese Academy of Sciences (CAS), Key Laboratory of Magnetic Materials and Devices, Zhejiang Engineering Research Center for Biomedical Materials, Ningbo Institute of Materials Technology and Engineering, CAS, Ningbo 315201, China; (H.A.-m.); (H.D.); (J.Y.); (H.P.); (C.Y.); (B.J.)
- College of Materials Sciences and Opto-Electronic Technology, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chenyang Yao
- Cixi Institute of Biomedical Engineering, International Cooperation Base of Biomedical Materials Technology and Application, Chinese Academy of Sciences (CAS), Key Laboratory of Magnetic Materials and Devices, Zhejiang Engineering Research Center for Biomedical Materials, Ningbo Institute of Materials Technology and Engineering, CAS, Ningbo 315201, China; (H.A.-m.); (H.D.); (J.Y.); (H.P.); (C.Y.); (B.J.)
- College of Materials Sciences and Opto-Electronic Technology, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Bo Jiang
- Cixi Institute of Biomedical Engineering, International Cooperation Base of Biomedical Materials Technology and Application, Chinese Academy of Sciences (CAS), Key Laboratory of Magnetic Materials and Devices, Zhejiang Engineering Research Center for Biomedical Materials, Ningbo Institute of Materials Technology and Engineering, CAS, Ningbo 315201, China; (H.A.-m.); (H.D.); (J.Y.); (H.P.); (C.Y.); (B.J.)
| | - Aiguo Wu
- Cixi Institute of Biomedical Engineering, International Cooperation Base of Biomedical Materials Technology and Application, Chinese Academy of Sciences (CAS), Key Laboratory of Magnetic Materials and Devices, Zhejiang Engineering Research Center for Biomedical Materials, Ningbo Institute of Materials Technology and Engineering, CAS, Ningbo 315201, China; (H.A.-m.); (H.D.); (J.Y.); (H.P.); (C.Y.); (B.J.)
- Advanced Energy Science and Technology Guangdong Laboratory, Huizhou 516000, China
| | - Fang Yang
- Cixi Institute of Biomedical Engineering, International Cooperation Base of Biomedical Materials Technology and Application, Chinese Academy of Sciences (CAS), Key Laboratory of Magnetic Materials and Devices, Zhejiang Engineering Research Center for Biomedical Materials, Ningbo Institute of Materials Technology and Engineering, CAS, Ningbo 315201, China; (H.A.-m.); (H.D.); (J.Y.); (H.P.); (C.Y.); (B.J.)
- Advanced Energy Science and Technology Guangdong Laboratory, Huizhou 516000, China
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41
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Novel Thiadiazole-Based Molecules as Promising Inhibitors of Black Fungi and Pathogenic Bacteria: In Vitro Antimicrobial Evaluation and Molecular Docking Studies. Molecules 2022; 27:molecules27113613. [PMID: 35684551 PMCID: PMC9182183 DOI: 10.3390/molecules27113613] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 05/29/2022] [Accepted: 06/02/2022] [Indexed: 02/01/2023] Open
Abstract
Novel 1,3,4-thiadiazole derivatives were synthesized through the reaction of methyl 2-(4-hydroxy-3-methoxybenzylidene) hydrazine-1-carbodithioate and the appropriate hydrazonoyl halides in the presence of a few drops of diisopropylethylamine. The chemical structure of the newly fabricated compounds was inferred from their microanalytical and spectral data. With the increase in microbial diseases, fungi remain a devastating threat to human health because of the resistance of microorganisms to antifungal drugs. COVID-19-associated pulmonary aspergillosis (CAPA) and COVID-19-associated mucormycosis (CAM) have higher mortality rates in many populations. The present study aimed to find new antifungal agents using the disc diffusion method, and minimal inhibitory concentration (MIC) values were estimated by the microdilution assay. An in vitro experiment of six synthesized chemical compounds exhibited antifungal activity against Rhizopus oryzae; compounds with an imidazole moiety, such as the compound 7, were documented to have energetic antibacterial, antifungal properties. As a result of these findings, this research suggests that the synthesized compounds could be an excellent choice for controlling black fungus diseases. Furthermore, a molecular docking study was achieved on the synthesized compounds, of which compounds 2, 6, and 7 showed the best interactions with the selected protein targets.
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Simó C, Fornari T, García-Risco MR, Peña-Cearra A, Abecia L, Anguita J, Rodríguez H, García-Cañas V. Resazurin-based high-throughput screening method for the discovery of dietary phytochemicals to target microbial transformation of L-carnitine into trimethylamine, a gut metabolite associated with cardiovascular disease. Food Funct 2022; 13:5640-5653. [PMID: 35506542 DOI: 10.1039/d2fo00103a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Nowadays, there is great interest in the discovery of food compounds that might inhibit gut microbial TMA production from its methylamine precursors. In this work, an innovative novel screening strategy capable of rapidly determining the differences in the metabolic response of Klebsiella pneumoniae, a bacteria producing TMA under aerobic conditions, to a library of extracts obtained from food and natural sources was developed. The proposed high-throughput screening (HTS) method combines resazurin reduction assay in 384-well plates and Gaussian Processes as a machine learning tool for data processing, allowing for a fast, cheap and highly standardized evaluation of any interfering effect of a given compound or extract on the microbial metabolism sustained by L-carnitine utilization. As a proof-of-concept of this strategy, a pilot screening of 39 extracts and 6 pure compounds was performed to search for potential candidates that could inhibit in vitro TMA formation from L-carnitine. Among all the extracts tested, three of them were selected as candidates to interfere with TMA formation. Subsequent in vitro assays confirmed the potential of oregano and red thyme hexane extracts (at 1 mg mL-1) to inhibit TMA formation in bacterial lysates. In such in vitro assay, the red thyme extract exerted comparable effects on TMA reduction (∼40%) as 7.5 mM meldonium (∼50% TMA decrease), a reported L-carnitine analogue. Our results show that metabolic activity could be used as a proxy of the capacity to produce TMA under controlled culture conditions using L-carnitine to sustain metabolism.
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Affiliation(s)
- Carolina Simó
- Molecular Nutrition and Metabolism, Institute of Food Science Research (CIAL), Spanish National Research Council (CSIC), Madrid, 28049, Spain.
| | - Tiziana Fornari
- Institute of Food Science Research (CIAL), Autonomous University of Madrid, Madrid, 28049, Spain
| | - Mónica R García-Risco
- Institute of Food Science Research (CIAL), Autonomous University of Madrid, Madrid, 28049, Spain
| | - Ainize Peña-Cearra
- CIC bioGUNE. Bizkaia Science and Technology Park, bld 801 A, 48160, Derio, Bizkaia, Spain.,Immunology, Microbiology and Parasitology Department, Medicine and Nursing Faculty, University of the Basque Country (UPV), 48940, Leioa, Spain
| | - Leticia Abecia
- CIC bioGUNE. Bizkaia Science and Technology Park, bld 801 A, 48160, Derio, Bizkaia, Spain.,Immunology, Microbiology and Parasitology Department, Medicine and Nursing Faculty, University of the Basque Country (UPV), 48940, Leioa, Spain
| | - Juan Anguita
- CIC bioGUNE. Bizkaia Science and Technology Park, bld 801 A, 48160, Derio, Bizkaia, Spain
| | - Héctor Rodríguez
- CIC bioGUNE. Bizkaia Science and Technology Park, bld 801 A, 48160, Derio, Bizkaia, Spain
| | - Virginia García-Cañas
- Molecular Nutrition and Metabolism, Institute of Food Science Research (CIAL), Spanish National Research Council (CSIC), Madrid, 28049, Spain.
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Glover G, Voliotis M, Łapińska U, Invergo BM, Soanes D, O'Neill P, Moore K, Nikolic N, Petrov PG, Milner DS, Roy S, Heesom K, Richards TA, Tsaneva-Atanasova K, Pagliara S. Nutrient and salt depletion synergistically boosts glucose metabolism in individual Escherichia coli cells. Commun Biol 2022; 5:385. [PMID: 35444215 PMCID: PMC9021252 DOI: 10.1038/s42003-022-03336-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 03/30/2022] [Indexed: 12/16/2022] Open
Abstract
The interaction between a cell and its environment shapes fundamental intracellular processes such as cellular metabolism. In most cases growth rate is treated as a proximal metric for understanding the cellular metabolic status. However, changes in growth rate might not reflect metabolic variations in individuals responding to environmental fluctuations. Here we use single-cell microfluidics-microscopy combined with transcriptomics, proteomics and mathematical modelling to quantify the accumulation of glucose within Escherichia coli cells. In contrast to the current consensus, we reveal that environmental conditions which are comparatively unfavourable for growth, where both nutrients and salinity are depleted, increase glucose accumulation rates in individual bacteria and population subsets. We find that these changes in metabolic function are underpinned by variations at the translational and posttranslational level but not at the transcriptional level and are not dictated by changes in cell size. The metabolic response-characteristics identified greatly advance our fundamental understanding of the interactions between bacteria and their environment and have important ramifications when investigating cellular processes where salinity plays an important role.
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Affiliation(s)
- Georgina Glover
- Living Systems Institute, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK
- Department of Physics and Astronomy, University of Exeter, Stocker Road, Exeter, EX4 4QL, UK
| | - Margaritis Voliotis
- Living Systems Institute, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK
- Department of Mathematics, University of Exeter, Stocker Road, Exeter, UK
| | - Urszula Łapińska
- Living Systems Institute, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK
- Biosciences, University of Exeter, Stocker Road, Exeter, EX4 4Q, UK
| | - Brandon M Invergo
- Translational Research Exchange at Exeter, University of Exeter, Exeter, UK
| | - Darren Soanes
- Biosciences, University of Exeter, Stocker Road, Exeter, EX4 4Q, UK
| | - Paul O'Neill
- Biosciences, University of Exeter, Stocker Road, Exeter, EX4 4Q, UK
| | - Karen Moore
- Biosciences, University of Exeter, Stocker Road, Exeter, EX4 4Q, UK
| | - Nela Nikolic
- Living Systems Institute, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK
- Institute of Science and Technology Austria, 3400, Klosterneuburg, Austria
| | - Peter G Petrov
- Department of Physics and Astronomy, University of Exeter, Stocker Road, Exeter, EX4 4QL, UK
| | - David S Milner
- Department of Zoology, University of Oxford, 11a Mansfield Road, Oxford, OX1 3SZ, UK
| | - Sumita Roy
- Living Systems Institute, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK
- Biosciences, University of Exeter, Stocker Road, Exeter, EX4 4Q, UK
| | - Kate Heesom
- University of Bristol Proteomics Facility, University Walk, Bristol, BS8 1TD, UK
| | - Thomas A Richards
- Department of Zoology, University of Oxford, 11a Mansfield Road, Oxford, OX1 3SZ, UK
| | - Krasimira Tsaneva-Atanasova
- Living Systems Institute, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK
- Department of Mathematics, University of Exeter, Stocker Road, Exeter, UK
- Department of Bioinformatics and Mathematical Modelling, Institute of Biophysics and Biomedical Engineering, Bulgarian Academy of Sciences, 105 Acad. G. Bonchev Str., 1113, Sofia, Bulgaria
| | - Stefano Pagliara
- Living Systems Institute, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK.
- Biosciences, University of Exeter, Stocker Road, Exeter, EX4 4Q, UK.
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44
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Gallegos-Martínez S, Lara-Mayorga IM, Samandari M, Mendoza-Buenrostro C, Flores-Garza BG, Reyes-Cortés L, Segoviano-Ramírez JC, Zhang YS, Trujillo de Santiago G, Alvarez MM. Culture of cancer spheroids and evaluation of anti-cancer drugs in 3D-printed miniaturized continuous stirred tank reactors (mCSTR). Biofabrication 2022; 14. [PMID: 35344936 DOI: 10.1088/1758-5090/ac61a4] [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: 09/29/2021] [Accepted: 03/28/2022] [Indexed: 11/11/2022]
Abstract
Cancer continues to be a leading cause of mortality in modern societies; therefore, improved and more reliable in vitro cancer models are needed to expedite fundamental research and anti-cancer drug development. Here, we describe the use of a miniaturized continuous stirred tank reactor (mCSTR) to first fabricate and mature cancer spheroids (i.e, derived from MCF7 cells, DU145 cells, and a mix of MCF7 cells and fibroblasts), and then to conduct anti-cancer drug assays under continuous perfusion. This 3 mL mCSTR features an off-center agitation system that enables homogeneous chaotic laminar mixing at low speeds to support cell aggregation. We incubated cell suspensions for 3 days in ultra-low-adherence (ULA) plates to allow formation of discoid cell aggregates (~600 µm in diameter). These cell aggregates were then transferred into mCSTRs and continuously fed with culture medium. We characterized the spheroid morphology and the expression of relevant tumor biomarkers at different maturation times for up to 4 weeks. The spheroids progressively increased in size during the first 5 to 6 days of culture to reach a steady diameter between 600 and 800 µm. In proof-of-principle experiments, we demonstrated the use of this mCSTR in anti-cancer drug testing. Three drugs commonly used in breast cancer treatment (doxorubicin, docetaxel, and paclitaxel) were probed at different concentrations in MCF7 derived spheroids. In these experiments, we evaluated cell viability, glucose consumption, spheroid morphology, lactate dehydrogenase activity, and the expression of genes associated with drug resistance (ABCB1 and ABCC1) and anti-apoptosis (Bcl2). We envision the use of this agitated system as a tumor-on-a-chip platform to expedite efficacy and safety testing of novel anti-cancer drugs and possibly in personalized medicine applications.
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Affiliation(s)
- Salvador Gallegos-Martínez
- Centro de Biotecnología-FEMSA, Tecnologico de Monterrey, Ave. Eugenio Garza Sada 2501 sur, Col. Tecnológico, Monterrey, Monterrey, Nuevo Leon, 64849, MEXICO
| | - Itzel Montserrat Lara-Mayorga
- Centro de Biotecnología-FEMSA, Tecnologico de Monterrey, Ave. Eugenio Garza Sada 2501 sur, Col. Tecnológico, Monterrey, Monterrey, Nuevo Leon, 64849, MEXICO
| | - Mohamadmahdi Samandari
- University of Connecticut Health Center, 263 Farmington Avenue, Farmington, Connecticut, 06032-1941, UNITED STATES
| | - Christian Mendoza-Buenrostro
- Centro de Innovación en Diseño y Tecnología, Tecnologico de Monterrey, Ave. Eugenio Garza Sada 2501 sur, Monterrey, Nuevo León, 64849, MEXICO
| | - Brenda Giselle Flores-Garza
- Centro de Biotecnología-FEMSA, Tecnologico de Monterrey, Ave. Eugenio Garza Sada 2501 sur, Col. Tecnológico, Monterrey, Monterrey, Nuevo Leon, 64849, MEXICO
| | - Luisa Reyes-Cortés
- Centro de Biotecnología-FEMSA, Tecnologico de Monterrey, Ave. Eugenio Garza Sada 2501 sur, Col. Tecnológico, Monterrey, Monterrey, Nuevo Leon, 64849, MEXICO
| | - Juan Carlos Segoviano-Ramírez
- Centro de Investigación y Desarrollo en Ciencias de la Salud, Universidad Autonoma de Nuevo Leon, Dr. José Eleuterio González (Gonzalitos), Mitras Centro, San Nicolas de los Garza, Nuevo Leon, 64460, MEXICO
| | - Yu Shrike Zhang
- Harvard Medical School, 65 Landsdowne Street, Boston, Massachusetts, 02115, UNITED STATES
| | - Grissel Trujillo de Santiago
- Centro de Biotecnología-FEMSA, Tecnologico de Monterrey, Ave. Eugenio Garza Sada 2501 sur, Col. Tecnológico, Monterrey, Monterrey, Nuevo Leon, 64849, MEXICO
| | - Mario Moisés Alvarez
- Centro de Biotecnología-FEMSA, Tecnologico de Monterrey, Ave. Eugenio Garza Sada 2501 sur, Col. Tecnológico, Monterrey, Monterrey, Nuevo Leon, 64849, MEXICO
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Matveeva VG, Senokosova EA, Sevostianova VV, Khanova MY, Glushkova TV, Akentieva TN, Antonova LV, Barbarash LS. Advantages of Fibrin Polymerization Method without the Use of Exogenous Thrombin for Vascular Tissue Engineering Applications. Biomedicines 2022; 10:biomedicines10040789. [PMID: 35453539 PMCID: PMC9026760 DOI: 10.3390/biomedicines10040789] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 03/16/2022] [Accepted: 03/25/2022] [Indexed: 01/01/2023] Open
Abstract
Fibrin is widely used in vascular tissue engineering. Typically, fibrin polymerization is initiated by adding exogenous thrombin. In this study, we proposed a protocol for the preparation of completely autologous fibrin without the use of endogenous thrombin and compared the properties of the prepared fibrin matrix with that obtained by the traditional method. Fibrinogen was obtained by ethanol precipitation followed by fibrin polymerization by adding either exogenous thrombin and calcium chloride (ExThr), or only calcium chloride (EnThr). We examined the structure, mechanical properties, thrombogenicity, degradation rate and cytocompatibility of fibrin matrices. Factor XIII (FXIII) quantitative assay was performed by ELISA, and FXIII activity was assessed by SDS-PAGE detection of γ-γ cross-links. The results show that network structure of EnThr fibrin was characterized by thinner fibers. The EnThr fibrin matrices had higher strength, stiffness and resistance to proteolytic degradation compared to ExThr fibrin. EnThr fibrin matrices exhibited less thrombogenicity in vitro than ExThr, and retained high cytocompatibility. Thus, the proposed approach has several advantages over the traditional method, namely the fabrication of a completely autologous coating material that has better mechanical properties, higher resistance to proteolysis and lower thrombogenicity.
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46
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Interrogation of Essentiality in the Reconstructed Haemophilus influenzae Metabolic Network Identifies Lipid Metabolism Antimicrobial Targets: Preclinical Evaluation of a FabH β-Ketoacyl-ACP Synthase Inhibitor. mSystems 2022; 7:e0145921. [PMID: 35293791 PMCID: PMC9040583 DOI: 10.1128/msystems.01459-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Expediting drug discovery to fight antibacterial resistance requires holistic approaches at system levels. In this study, we focused on the human-adapted pathogen Haemophilus influenzae, and by constructing a high-quality genome-scale metabolic model, we rationally identified new metabolic drug targets in this organism. Contextualization of available gene essentiality data within in silico predictions identified most genes involved in lipid metabolism as promising targets. We focused on the β-ketoacyl-acyl carrier protein synthase III FabH, responsible for catalyzing the first step in the FASII fatty acid synthesis pathway and feedback inhibition. Docking studies provided a plausible three-dimensional model of FabH in complex with the synthetic inhibitor 1-(5-(2-fluoro-5-(hydroxymethyl)phenyl)pyridin-2-yl)piperidine-4-acetic acid (FabHi). Validating our in silico predictions, FabHi reduced H. influenzae viability in a dose- and strain-dependent manner, and this inhibitory effect was independent of fabH gene expression levels. fabH allelic variation was observed among H. influenzae clinical isolates. Many of these polymorphisms, relevant for stabilization of the dimeric active form of FabH and/or activity, may modulate the inhibitory effect as part of a complex multifactorial process with the overall metabolic context emerging as a key factor tuning FabHi activity. Synergies with antibiotics were not observed and bacteria were not prone to develop resistance. Inhibitor administration during H. influenzae infection on a zebrafish septicemia infection model cleared bacteria without signs of host toxicity. Overall, we highlight the potential of H. influenzae metabolism as a source of drug targets, metabolic models as target-screening tools, and FASII targeting suitability to counteract this bacterial infection. IMPORTANCE Antimicrobial resistance drives the need of synergistically combined powerful computational tools and experimental work to accelerate target identification and drug development. Here, we present a high-quality metabolic model of H. influenzae and show its usefulness both as a computational framework for large experimental data set contextualization and as a tool to discover condition-independent drug targets. We focus on β-ketoacyl-acyl carrier protein synthase III FabH chemical inhibition by using a synthetic molecule with good synthetic and antimicrobial profiles that specifically binds to the active site. The mechanistic complexity of FabH inhibition may go beyond allelic variation, and the strain-dependent effect of the inhibitor tested supports the impact of metabolic context as a key factor driving bacterial cell behavior. Therefore, this study highlights the systematic metabolic evaluation of individual strains through computational frameworks to identify secondary metabolic hubs modulating drug response, which will facilitate establishing synergistic and/or more precise and robust antibacterial treatments.
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47
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Atakpa EO, Zhou H, Jiang L, Ma Y, Liang Y, Li Y, Zhang D, Zhang C. Improved degradation of petroleum hydrocarbons by co-culture of fungi and biosurfactant-producing bacteria. CHEMOSPHERE 2022; 290:133337. [PMID: 34933030 DOI: 10.1016/j.chemosphere.2021.133337] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 12/12/2021] [Accepted: 12/14/2021] [Indexed: 06/14/2023]
Abstract
Microbial remediation has proven to be an effective technique for the cleanup of crude-oil contaminated sites. However, limited information exists on the dynamics involved in defined co-cultures of biosurfactant-producing bacteria and fungi in bioremediation processes. In this study, a fungal strain (Scedosporium sp. ZYY) capable of degrading petroleum hydrocarbons was isolated and co-cultured with biosurfactant-producing bacteria (Acinetobacter sp. Y2) to investigate their combined effect on crude-oil degradation. Results showed that the surface tension of the co-culture decreased from 63.12 to 47.58 mN m-1, indicating the secretion of biosurfactants in the culture. Meanwhile, the degradation rate of total petroleum hydrocarbon increased from 23.36% to 58.61% at the end of the 7-d incubation period. In addition, gas chromatography - mass spectrometry analysis showed a significant (P < 0.05) degradation from 3789.27 mg/L to 940.33 mg/L for n-alkanes and 1667.33 μg/L to 661.5 μg/L for polycyclic aromatic hydrocarbons. Moreover, RT-qPCR results revealed the high expression of alkB and CYP52 genes by Acinetobacter sp. Y2 and Scedosporium sp. ZYY respectively in the co-culture, which corelated positively (P < 0.01) with n-alkane removal. Finally, microbial growth assay which corresponded with Fluorescein diacetate hydrolysis activity, highlighted the synergistic behavior of both strains in tackling the crude oil. Findings in this study suggest that the combination of fungal strain and biosurfactant-producing bacteria effectively enhances the degradation of petroleum hydrocarbons, which could shed new light on the improvement of bioremediation strategies.
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Affiliation(s)
- Edidiong Okokon Atakpa
- Institute of Marine Biology and Pharmacology, Ocean College, Zhejiang University, Zhoushan, 316021, Zhejiang, China
| | - Hanghai Zhou
- Institute of Marine Biology and Pharmacology, Ocean College, Zhejiang University, Zhoushan, 316021, Zhejiang, China
| | - Lijia Jiang
- Institute of Marine Biology and Pharmacology, Ocean College, Zhejiang University, Zhoushan, 316021, Zhejiang, China
| | - Yinghui Ma
- Microbiology Institute of Shaanxi, Xi'an, 710043, Shaanxi, China
| | - Yanpeng Liang
- College of Environmental Science and Engineering, Guilin University of Technology, Guilin, 541006, China
| | - Yanhong Li
- College of Environmental Science and Engineering, Guilin University of Technology, Guilin, 541006, China
| | - Dongdong Zhang
- Institute of Marine Biology and Pharmacology, Ocean College, Zhejiang University, Zhoushan, 316021, Zhejiang, China
| | - Chunfang Zhang
- Institute of Marine Biology and Pharmacology, Ocean College, Zhejiang University, Zhoushan, 316021, Zhejiang, China.
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48
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Boutsioukis C, Arias-Moliz MT, Chávez de Paz LE. A critical analysis of research methods and experimental models to study irrigants and irrigation systems. Int Endod J 2022; 55 Suppl 2:295-329. [PMID: 35171506 PMCID: PMC9314845 DOI: 10.1111/iej.13710] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 02/07/2022] [Accepted: 02/08/2022] [Indexed: 11/28/2022]
Abstract
Irrigation plays an essential role in root canal treatment. The purpose of this narrative review was to critically appraise the experimental methods and models used to study irrigants and irrigation systems and to provide directions for future research. Studies on the antimicrobial effect of irrigants should use mature multispecies biofilms grown on dentine or inside root canals and should combine at least two complementary evaluation methods. Dissolution of pulp tissue remnants should be examined in the presence of dentine and, preferably, inside human root canals. Micro-omputed tomography is currently the method of choice for the assessment of accumulated dentine debris and their removal. A combination of experiments in transparent root canals and numerical modeling is needed to address irrigant penetration. Finally, models to evaluate irrigant extrusion through the apical foramen should simulate the periapical tissues and provide quantitative data on the amount of extruded irrigant. Mimicking the in vivo conditions as close as possible and standardization of the specimens and experimental protocols are universal requirements irrespective of the surrogate endpoint studied. Obsolete and unrealistic models must be abandoned in favour of more appropriate and valid ones that have more direct application and translation to clinical Endodontics.
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Affiliation(s)
- C Boutsioukis
- Department of Endodontology, Academic Centre for Dentistry Amsterdam (ACTA), University of Amsterdam and Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - M T Arias-Moliz
- Department of Microbiology, Faculty of Dentistry, University of Granada, Granada, Spain
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49
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Touchette D, Altshuler I, Raymond-Bouchard I, Fernández-Martínez MÁ, Bourdages LJ, O'Connor B, Ricco AJ, Whyte LG. Microfluidics Microbial Activity MicroAssay: An Automated In Situ Microbial Metabolic Detection System. ASTROBIOLOGY 2022; 22:158-170. [PMID: 35049343 DOI: 10.1089/ast.2021.0072] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
With no direct extant-life detection instrumentation included in a space mission since the 1970s, the advancement of new technologies to be included in future space missions is imperative. We developed, optimized, and tested a semi-automated prototype, the microfluidics Microbial Activity MicroAssay (μMAMA). This system metabolically characterizes and detects extant microbial life by way of metabolism-indicator redox dyes. We first evaluated the robustness and sensitivity of six redox dye/buffer combinations, and we then tested their responses to metabolic activity in astrobiological analog high-Arctic samples. We determined that the Biolog Inoculating Fluid (IF)-C and AlamarBlue buffered in IF-0a (aB-IF0a) dye/buffer combinations were optimal, as they detected metabolic activity from the fewest microbial cells (102 cells/mL) while maintaining efficacy over a broad physiochemical range of pH (0-13), temperature (-10°C to 37°C), salinity and perchlorate (tested up to 30%), and in the presence of a Mars regolith simulant (MMS-2). The μMAMA, which incorporated these redox dyes, detected extant active cold-adapted microbial life from high Arctic analog sites, including samples amended with substrates targeting chemolithoautotrophic metabolisms. Given μMAMA's small size (we estimate a complete planetary instrument could occupy as little as 3 L) and potential for automation, it could easily be incorporated into almost any landed platform for life detection missions.
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Affiliation(s)
- David Touchette
- Department of Natural Resource Sciences, McGill University, Sainte-Anne-de-Bellevue, Québec, Canada
- McGill Space Institute, Montréal, Québec, Canada
| | - Ianina Altshuler
- Department of Natural Resource Sciences, McGill University, Sainte-Anne-de-Bellevue, Québec, Canada
- Department of Animal and Aquaculture Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway
| | - Isabelle Raymond-Bouchard
- Department of Natural Resource Sciences, McGill University, Sainte-Anne-de-Bellevue, Québec, Canada
- McGill Space Institute, Montréal, Québec, Canada
| | - Miguel Ángel Fernández-Martínez
- Department of Natural Resource Sciences, McGill University, Sainte-Anne-de-Bellevue, Québec, Canada
- McGill Space Institute, Montréal, Québec, Canada
| | - Louis-Jacques Bourdages
- Department of Natural Resource Sciences, McGill University, Sainte-Anne-de-Bellevue, Québec, Canada
- Department of Mechanical Engineering, Faculty of Engineering, McGill University, Montréal, Québec, Canada
| | - Brady O'Connor
- Department of Natural Resource Sciences, McGill University, Sainte-Anne-de-Bellevue, Québec, Canada
- McGill Space Institute, Montréal, Québec, Canada
| | | | - Lyle G Whyte
- Department of Natural Resource Sciences, McGill University, Sainte-Anne-de-Bellevue, Québec, Canada
- McGill Space Institute, Montréal, Québec, Canada
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Lindivat M, Bratbak G, Larsen A, Hess-Erga OK, Hoell IA. Flow Cytometric Analysis of Bacterial Protein Synthesis: Monitoring Vitality After Water Treatment. Front Microbiol 2021; 12:772651. [PMID: 34956134 PMCID: PMC8702973 DOI: 10.3389/fmicb.2021.772651] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 11/12/2021] [Indexed: 11/13/2022] Open
Abstract
Bacterial vitality after water disinfection treatment was investigated using bio-orthogonal non-canonical amino acid tagging (BONCAT) and flow cytometry (FCM). Protein synthesis activity and DNA integrity (BONCAT–SYBR Green) was monitored in Escherichia coli monocultures and in natural marine samples after UV irradiation (from 25 to 200 mJ/cm2) and heat treatment (from 15 to 45 min at 55°C). UV irradiation of E. coli caused DNA degradation followed by the decrease in protein synthesis within a period of 24 h. Heat treatment affected both DNA integrity and protein synthesis immediately, with an increased effect over time. Results from the BONCAT method were compared with results from well-known methods such as plate counts (focusing on growth) and LIVE/DEAD™ BacLight™ (focusing on membrane permeability). The methods differed somewhat with respect to vitality levels detected in bacteria after the treatments, but the results were complementary and revealed that cells maintained metabolic activity and membrane integrity despite loss of cell division. Similarly, analysis of protein synthesis in marine bacteria with BONCAT displayed residual activity despite inability to grow or reproduce. Background controls (time zero blanks) prepared using different fixatives (formaldehyde, isopropanol, and acetic acid) and several different bacterial strains revealed that the BONCAT protocol still resulted in labeled, i.e., apparently active, cells. The reason for this is unclear and needs further investigation to be understood. Our results show that BONCAT and FCM can detect, enumerate, and differentiate bacterial cells after physical water treatments such as UV irradiation and heating. The method is reliable to enumerate and explore vitality of single cells, and a great advantage with BONCAT is that all proteins synthesized within cells are analyzed, compared to assays targeting specific elements such as enzyme activity.
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Affiliation(s)
- Mathilde Lindivat
- Faculty of Engineering and Science, Institute of Safety, Chemistry and Biomedical Laboratory Sciences, Western Norway University of Applied Sciences, Haugesund, Norway
| | - Gunnar Bratbak
- Department of Biological Sciences, University of Bergen, Bergen, Norway
| | - Aud Larsen
- Department of Biological Sciences, University of Bergen, Bergen, Norway.,NORCE Environment, NORCE Norwegian Research Center AS, Bergen, Norway
| | | | - Ingunn Alne Hoell
- Faculty of Engineering and Science, Institute of Safety, Chemistry and Biomedical Laboratory Sciences, Western Norway University of Applied Sciences, Haugesund, Norway
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