1
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Park K, Kim KY, Kirk MF, Kwon MJ. Biofilm development on fractured rock in oligotrophic nitrate-rich groundwater: An in-situ bioreactor study. WATER RESEARCH 2025; 277:123329. [PMID: 39985993 DOI: 10.1016/j.watres.2025.123329] [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: 12/08/2024] [Revised: 02/13/2025] [Accepted: 02/18/2025] [Indexed: 02/24/2025]
Abstract
Biofilms drive all biogeochemical processes and represent the main mode of existence for active microbial life. Many past studies examined biofilm formation under static and eutrophic conditions, but those conditions are not representative of typical groundwater environments. In this study, we developed in situ bioreactors and methodologies to examine the influence of subsurface properties such as redox condition and lithology on the properties of naturally formed biofilms in two adjacent wells, a 30-m deep well completed in alluvium and a 120-m deep well in gneiss bedrock. The bulk chemistry of groundwater from the wells was similar, with neutral pH and abundant nitrate (21.9-24.6 mg/L), but redox conditions differed with depth (alluvial: oxic, gneiss bedrock: anoxic). Microbial community analysis revealed distinct clustering of biofilm community composition with the groundwater environment. Biofilm communities were consistently assembled by deterministic processes whereas planktonic communities had a higher influence of stochastic processes. Alluvial biofilms exhibited more diverse communities mainly composed of organotrophic aerobes capable of nitrate utilization. Bedrock biofilms indicated similar community compositions with groundwater where anaerobic denitrifiers coupled with sulfur oxidizers were dominant. Visualization and biomass quantification revealed distinct morphologies and development of biofilm along rock types and groundwater environments. Biofilm on gneiss surface had more biomass and formed a thin layered structure, compared to sandstone biofilm which had a randomly distributed pattern, implying that the morphology of biofilm was governed by the properties of the rock. Attached to unattached (planktonic) microbe ratios ranged from 3.9 × 103 to 1.2 × 104: 1 in the gneiss surface and 3.4 × 102 to 4.2 × 102: 1 in the sandstone surface in bedrock groundwater environment. Taken together, this study advances our understanding of subsurface biomass abundance and demonstrates that the in-situ bioreactors are effective for cultivating and analyzing of subsurface biofilms. Based on the specific field conditions tested, we found that biofilm can form stably on fractured rock surfaces within a year, with groundwater redox conditions shaping community composition and rock types determining biofilm volume and morphology. The methodologies presented here can be extended to other subsurface environments with varying groundwater geochemistry and lithology, which will help further refine estimates of microbial life and its role in subsurface ecosystems.
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Affiliation(s)
- Kanghyun Park
- Department of Earth and Environmental Sciences, Korea University, Seoul 02841, South Korea
| | - Kue-Young Kim
- Korea Institute of Geoscience and Mineral Resources (KIGAM), Daejeon 34132, South Korea
| | - Matthew F Kirk
- Department of Geology, Kansas State University, Manhattan, KS 66506, United States
| | - Man Jae Kwon
- Department of Earth and Environmental Sciences, Korea University, Seoul 02841, South Korea.
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2
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Gurevich VV. Assembling the jigsaw puzzle of life. Trends Biochem Sci 2025; 50:374-375. [PMID: 40102125 PMCID: PMC12048255 DOI: 10.1016/j.tibs.2025.02.003] [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: 11/12/2024] [Revised: 02/07/2025] [Accepted: 02/21/2025] [Indexed: 03/20/2025]
Abstract
The cell is a dynamic system where millions of molecules of thousands different kinds act within a complex network with numerous feedback loops. Because we cannot pursue many targets simultaneously, 'big data' rarely yield useful leads. Comprehensive models can place the snippets obtained in simplified experimental conditions into a coherent picture.
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Affiliation(s)
- Vsevolod V Gurevich
- Department of Pharmacology, Vanderbilt University, Nashville, TN 27232, USA.
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3
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Echenique-Subiabre I, Jackrel SL, McCarren J, James CC, Perez-Coronel E, Tran C, Perreault M, Farah U, White PS, Baker HK, Wall CB, Sager L, Becker S, Barton AD, Shurin JB. Traits determine dispersal and colonization abilities of microbes. Appl Environ Microbiol 2025; 91:e0205524. [PMID: 39976438 PMCID: PMC11921345 DOI: 10.1128/aem.02055-24] [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: 10/28/2024] [Accepted: 12/19/2024] [Indexed: 02/21/2025] Open
Abstract
Many microbes disperse through the air, yet the phenotypic traits that enhance or constrain aerial dispersal or allow successful colonization of new habitats are poorly understood. We used a metabarcoding bacterial and eukaryotic data set to explore the trait structures of the aquatic, terrestrial, and airborne microbial communities near the Salton Sea, California, as well as those colonizing a series of experimental aquatic mesocosms. We assigned taxonomic identities to amplicon sequence variants (ASVs) and matched them to functional trait values through published papers and databases that infer phenotypic and/or metabolic traits information from taxonomy. We asked what traits distinguish successful microbial dispersers and/or colonizers from terrestrial and aquatic source communities. Our study found broad differences in taxonomic and trait composition between dispersers and colonizers compared to the source soil and water communities. Dispersers were characterized by larger cell diameters, colony formation, and fermentation abilities, while colonizers tended to be phototrophs that form mucilage and have siliceous coverings. Shorter population doubling times, spore-, and/or cyst-forming organisms were more abundant among the dispersers and colonizers than the sources. These results show that the capacity for aerial dispersal and colonization varies among microbial functional groups and taxa and is related to traits that affect other functions like resource acquisition, predator avoidance, and reproduction. The ability to disperse and colonize new habitats may therefore distinguish microbial guilds based on tradeoffs among alternate ecological strategies.IMPORTANCEMicrobes have long been thought to disperse rapidly across biogeographic barriers; however, whether dispersal or colonization vary among taxa or groups or is related to cellular traits remains unknown. We use a novel approach to understand how microorganisms disperse and establish themselves in different environments by looking at their traits (physiology, morphology, life history, and behavior characteristics). By collecting samples from habitats including water, soil, and the air and colonizing experimental tanks, we found dispersal and invasion vary among microorganisms. Some taxa and functional groups are found more often in the air or colonizing aquatic environments, while others that are commonly found in the soil or water rarely disperse or invade new habitat. Interestingly, the traits that help microorganisms survive and thrive also play a role in their ability to disperse and colonize. These findings have significant implications for understanding microorganisms' success and adaptation to new environments.
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Affiliation(s)
- Isidora Echenique-Subiabre
- Department of Ecology, Behavior & Evolution, University of California San Diego, La Jolla, California, USA
| | - Sara L. Jackrel
- Department of Ecology, Behavior & Evolution, University of California San Diego, La Jolla, California, USA
| | | | - Chase C. James
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
| | - Elisabet Perez-Coronel
- Department of Ecology, Behavior & Evolution, University of California San Diego, La Jolla, California, USA
| | - Cindy Tran
- Department of Ecology, Behavior & Evolution, University of California San Diego, La Jolla, California, USA
| | - Madeline Perreault
- Department of Ecology, Behavior & Evolution, University of California San Diego, La Jolla, California, USA
| | - Ugbad Farah
- Department of Ecology, Behavior & Evolution, University of California San Diego, La Jolla, California, USA
| | - P. Signe White
- Department of Ecology, Behavior & Evolution, University of California San Diego, La Jolla, California, USA
| | - Henry K. Baker
- Department of Ecology, Behavior & Evolution, University of California San Diego, La Jolla, California, USA
| | - Christopher B. Wall
- Department of Ecology, Behavior & Evolution, University of California San Diego, La Jolla, California, USA
| | | | | | - Andrew D. Barton
- Department of Ecology, Behavior & Evolution, University of California San Diego, La Jolla, California, USA
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
| | - Jonathan B. Shurin
- Department of Ecology, Behavior & Evolution, University of California San Diego, La Jolla, California, USA
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4
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Wood J, Palms D, Luu QT, Vasilev K, Bright R. Investigating Simulated Cellular Interactions on Nanostructured Surfaces with Antibacterial Properties: Insights from Force Curve Simulations. NANOMATERIALS (BASEL, SWITZERLAND) 2025; 15:462. [PMID: 40137635 PMCID: PMC11944641 DOI: 10.3390/nano15060462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2025] [Revised: 03/13/2025] [Accepted: 03/14/2025] [Indexed: 03/29/2025]
Abstract
This study investigates the simulation of interactions between cells and antibacterial nanostructured surfaces. Understanding the physical interaction forces between cells and nanostructured surfaces is crucial for developing antibacterial materials, yet existing physical models are limited. Force simulation studies can simplify analysis by focusing on mechanical interactions while disregarding factors such as bacterial deformation and complex biochemical signals. To simulate these interactions, Atomic Force Microscopy (AFM) was employed to generate force curves, allowing precise monitoring of the interaction between a 5 µm spherical cantilever tip and titanium alloy (Ti6Al4V) surfaces. AFM uniquely enables customized approaches and retraction cycles, providing detailed insights into attractive-repulsive forces across different surface morphologies. Two nanostructured surfaces, created via hydrothermal etching using KOH and NaOH, were compared to a Ti6Al4V control surface. Results demonstrated significant changes in nanomechanical properties due to surface chemistry and morphology. The Ti6Al4V control surface exhibited a 44 ± 5 N/m stiffness, which decreased to 20 ± 3 N/m on KOH-etched nanostructured (NS) surfaces and 29 ± 4 N/m on NaOH-etched NS surfaces. Additionally, surface energy decreased by magnitude on nanostructured surfaces compared to the control. The nature of interaction forces also varied: short-range forces were predominant on KOH-etched surfaces, while NaOH-etched surfaces exhibited stronger long-range forces. These findings provide valuable insights into how nanostructure patterning influences cell-like interactions, offering potential applications in antibacterial surface design. By tailoring nanomechanical properties through specific etching techniques, biomaterial performance can be optimized for clinical applications, enhancing antibacterial efficacy and reducing microbial adhesion.
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Affiliation(s)
- Jonathan Wood
- Academic Unit of STEM, University of South Australia, Adelaide, SA 5095, Australia;
| | - Dennis Palms
- College of Medicine and Public Health, Flinders University, Adelaide, SA 5042, Australia; (D.P.); (Q.T.L.); (K.V.)
| | - Quan Trong Luu
- College of Medicine and Public Health, Flinders University, Adelaide, SA 5042, Australia; (D.P.); (Q.T.L.); (K.V.)
| | - Krasimir Vasilev
- College of Medicine and Public Health, Flinders University, Adelaide, SA 5042, Australia; (D.P.); (Q.T.L.); (K.V.)
| | - Richard Bright
- College of Medicine and Public Health, Flinders University, Adelaide, SA 5042, Australia; (D.P.); (Q.T.L.); (K.V.)
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5
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Palmer JTT, Gerth ML. A Method for the Separation of Phytophthora Oosporesfrom Soil for DNA-Based Detection. Methods Mol Biol 2025; 2892:139-149. [PMID: 39729274 DOI: 10.1007/978-1-0716-4330-3_10] [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] [Indexed: 12/28/2024]
Abstract
Here, we present a protocol for the isolation and detection of Phytophthora oospores directly from soil samples. Our method incorporates a novel technique for isolating Phytophthora oospores using filter pouches and an improved DNA extraction procedure specifically designed for oospores. While we have primarily developed this protocol for detecting P. agathidicida oospores using end-point PCR, we believe these methods can be readily adapted for other Phytophthora species. Furthermore, the DNA extracted using this protocol is suitable as input for other DNA-based detection methods.
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Affiliation(s)
- Jade T T Palmer
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Monica L Gerth
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand.
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6
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Chimileski S, Borisy GG, Dewhirst FE, Mark Welch JL. Tip extension and simultaneous multiple fission in a filamentous bacterium. Proc Natl Acad Sci U S A 2024; 121:e2408654121. [PMID: 39226354 PMCID: PMC11406273 DOI: 10.1073/pnas.2408654121] [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: 04/30/2024] [Accepted: 07/29/2024] [Indexed: 09/05/2024] Open
Abstract
Organisms display an immense variety of shapes, sizes, and reproductive strategies. At microscopic scales, bacterial cell morphology and growth dynamics are adaptive traits that influence the spatial organization of microbial communities. In one such community-the human dental plaque biofilm-a network of filamentous Corynebacterium matruchotii cells forms the core of bacterial consortia known as hedgehogs, but the processes that generate these structures are unclear. Here, using live-cell time-lapse microscopy and fluorescent D-amino acids to track peptidoglycan biosynthesis, we report an extraordinary example of simultaneous multiple division within the domain Bacteria. We show that C. matruchotii cells elongate at one pole through tip extension, similar to the growth strategy of soil-dwelling Streptomyces bacteria. Filaments elongate rapidly, at rates more than five times greater than other closely related bacterial species. Following elongation, many septa form simultaneously, and each cell divides into 3 to 14 daughter cells, depending on the length of the mother filament. The daughter cells then nucleate outgrowth of new thinner vegetative filaments, generating the classic "whip handle" morphology of this taxon. Our results expand the known diversity of bacterial cell cycles and help explain how this filamentous bacterium can compete for space, access nutrients, and form important interspecies interactions within dental plaque.
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Affiliation(s)
- Scott Chimileski
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA02543
| | - Gary G. Borisy
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA02543
- Department of Microbiology, American Dental Association Forsyth Institute, Cambridge, MA02142
| | - Floyd E. Dewhirst
- Department of Microbiology, American Dental Association Forsyth Institute, Cambridge, MA02142
- Department of Oral Medicine, Infection and Immunity, Harvard School of Dental Medicine, Boston, MA02115
| | - Jessica L. Mark Welch
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA02543
- Department of Microbiology, American Dental Association Forsyth Institute, Cambridge, MA02142
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7
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Luther AM, Varzandeh M, Beckermann C, Feyer L, Maaßen IK, Oldenhof H, Hackbarth S, Waberski D. Fertility after photodynamic inactivation of bacteria in extended boar semen. Front Microbiol 2024; 15:1429749. [PMID: 39171264 PMCID: PMC11335528 DOI: 10.3389/fmicb.2024.1429749] [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: 05/08/2024] [Accepted: 07/23/2024] [Indexed: 08/23/2024] Open
Abstract
Antimicrobial resistance is an increasing challenge in semen preservation of breeding animals, especially in the porcine species. Bacteria are a natural component of semen, and their growth should be inhibited to protect sperm fertilizing capacity and the female's health. In pig breeding, where semen is routinely stored at 17°C in the liquid state, alternatives to conventional antibiotics are urgently needed. Photodynamic inactivation (PDI) of bacteria is a well-established tool in medicine and the food industry but this technology has not been widely adopted in semen preservation. The specific challenge in this setting is to selectively inactivate bacteria while maintaining sperm integrity and functionality. The aim of this study was to test the principle of PDI in liquid stored boar semen using the photosensitizer 5,10,15,20-tetrakis(N-methyl-4-pyridyl)-21H,23H-porphine (TMPyP) and a white light LED-setup. In the first step, photophysical experiments comprising singlet oxygen phosphorescence kinetics of TMPyP and determination of the photosensitizer triplet time revealed a sufficiently high production of reactive singlet oxygen in the Androstar Premium semen extender, whereas seminal plasma acted as strong quencher. In vitro experiments with extended boar semen showed that the established PDI protocol preserves sperm motility, membrane integrity, DNA integrity, and mitochondrial activity while efficiently reducing the bacteria below the detection limit. A proof-of-concept insemination study confirmed the in vivo fertility of semen after photodynamic treatment. In conclusion, using the PDI approach, an innovative tool was established that efficiently controls bacteria growth in extended boar and maintains sperm fertility. This could be a promising contribution to the One Health concept with the potential to reduce antimicrobial resistance in animal husbandry.
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Affiliation(s)
- Anne-Marie Luther
- Unit for Reproductive Medicine/Clinic for Swine and Small Ruminants, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Mohammad Varzandeh
- Photobiophysics, Institute of Physics, Humboldt University of Berlin, Berlin, Germany
| | - Christina Beckermann
- Unit for Reproductive Medicine/Clinic for Swine and Small Ruminants, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Leon Feyer
- Photobiophysics, Institute of Physics, Humboldt University of Berlin, Berlin, Germany
| | - Isabel Katharina Maaßen
- Unit for Reproductive Medicine/Clinic for Swine and Small Ruminants, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Harriёtte Oldenhof
- Unit for Reproductive Medicine/Clinic for Horses, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Steffen Hackbarth
- Photobiophysics, Institute of Physics, Humboldt University of Berlin, Berlin, Germany
| | - Dagmar Waberski
- Unit for Reproductive Medicine/Clinic for Swine and Small Ruminants, University of Veterinary Medicine Hannover, Hannover, Germany
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8
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Secaira-Morocho H, Chede A, Gonzalez-de-Salceda L, Garcia-Pichel F, Zhu Q. An evolutionary optimum amid moderate heritability in prokaryotic cell size. Cell Rep 2024; 43:114268. [PMID: 38776226 DOI: 10.1016/j.celrep.2024.114268] [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: 01/04/2024] [Revised: 04/11/2024] [Accepted: 05/08/2024] [Indexed: 05/24/2024] Open
Abstract
We investigate the distribution and evolution of prokaryotic cell size based on a compilation of 5,380 species. Size spans four orders of magnitude, from 100 nm (Mycoplasma) to more than 1 cm (Thiomargarita); however, most species congregate heavily around the mean. The distribution approximates but is distinct from log normality. Comparative phylogenetics suggests that size is heritable, yet the phylogenetic signal is moderate, and the degree of heritability is independent of taxonomic scale (i.e., fractal). Evolutionary modeling indicates the presence of an optimal cell size to which most species gravitate. The size is equivalent to a coccus of 0.70 μm in diameter. Analyses of 1,361 species with sequenced genomes show that genomic traits contribute to size evolution moderately and synergistically. Given our results, scaling theory, and empirical evidence, we discuss potential drivers that may expand or shrink cells around the optimum and propose a stability landscape model for prokaryotic cell size.
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Affiliation(s)
- Henry Secaira-Morocho
- Center for Fundamental and Applied Microbiomics and School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Abhinav Chede
- Center for Fundamental and Applied Microbiomics and School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Luis Gonzalez-de-Salceda
- Center for Fundamental and Applied Microbiomics and School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Ferran Garcia-Pichel
- Center for Fundamental and Applied Microbiomics and School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA.
| | - Qiyun Zhu
- Center for Fundamental and Applied Microbiomics and School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA.
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9
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Li X, Liu C, Wang D, Deng J, Guo Y, Shen Y, Yang S, Ji JS, Luo H, Bai J, Jiang J. Persistent pollution of genetic materials in a typical laboratory environment. JOURNAL OF HAZARDOUS MATERIALS 2024; 470:134201. [PMID: 38579585 DOI: 10.1016/j.jhazmat.2024.134201] [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: 12/26/2023] [Revised: 03/20/2024] [Accepted: 04/01/2024] [Indexed: 04/07/2024]
Abstract
From the onset of coronavirus disease (COVID-19) pandemic, there are concerns regarding the disease spread and environmental pollution of biohazard since studies on genetic engineering flourish and numerous genetic materials were used such as the nucleic acid test of the severe acute respiratory syndrome coronavirus (SARS-CoV-2). In this work, we studied genetic material pollution in an institute during a development cycle of plasmid, one of typical genetic materials, with typical laboratory settings. The pollution source, transmission routes, and pollution levels in laboratory environment were examined. The Real-Time quantitative- Polymerase Chain Reaction results of all environmental mediums (surface, aerosol, and liquid) showed that a targeted DNA segment occurred along with routine experimental operations. Among the 79 surface and air samples collected in the genetic material operation, half of the environment samples (38 of 79) are positive for nucleic acid pollution. Persistent nucleic acid contaminations were observed in all tested laboratories and spread in the public area (hallway). The highest concentration for liquid and surface samples were 1.92 × 108 copies/uL and 5.22 × 107 copies/cm2, respectively. Significant amounts of the targeted gene (with a mean value of 74 copies/L) were detected in the indoor air of laboratories utilizing centrifuge devices, shaking tables, and cell homogenizers. Spills and improper disposal of plasmid products were primary sources of pollution. The importance of establishing designated experimental zones, employing advanced biosafety cabinets, and implementing highly efficient cleaning systems in laboratories with lower biosafety levels is underscored. SYNOPSIS: STATEMENT. Persistent environmental pollutions of genetic materials are introduced by typical experiments in laboratories with low biosafety level.
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Affiliation(s)
- Xue Li
- School of Environment, Tsinghua University, Beijing, China
| | - Ce Liu
- School of Pharmaceutical Sciences, Tsinghua University, Beijing, China
| | - Dongbin Wang
- School of Environment, Tsinghua University, Beijing, China
| | - Jianguo Deng
- School of Environment, Tsinghua University, Beijing, China
| | - Yuntao Guo
- Department of Electrical Engineering, Tsinghua University, Beijing, China
| | - Yicheng Shen
- School of Environment, Tsinghua University, Beijing, China
| | - Shuwen Yang
- School of Environment, Tsinghua University, Beijing, China
| | - John S Ji
- Vanke School of Public Health, Tsinghua University, Beijing, China
| | - Haiyun Luo
- Department of Electrical Engineering, Tsinghua University, Beijing, China
| | - Jingwei Bai
- School of Pharmaceutical Sciences, Tsinghua University, Beijing, China
| | - Jingkun Jiang
- School of Environment, Tsinghua University, Beijing, China.
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10
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Adeleye SA, Yadavalli SS. Queuosine biosynthetic enzyme, QueE moonlights as a cell division regulator. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.10.31.565030. [PMID: 37961685 PMCID: PMC10635034 DOI: 10.1101/2023.10.31.565030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
In many organisms, stress responses to adverse environments can trigger secondary functions of certain proteins by altering protein levels, localization, activity, or interaction partners. Escherichia coli cells respond to the presence of specific cationic antimicrobial peptides by strongly activating the PhoQ/PhoP two-component signaling system, which regulates genes important for growth under this stress. As part of this pathway, a biosynthetic enzyme called QueE, which catalyzes a step in the formation of queuosine (Q) tRNA modification is upregulated. When cellular QueE levels are high, it co-localizes with the central cell division protein FtsZ at the septal site, blocking division and resulting in filamentous growth. Here we show that QueE affects cell size in a dose-dependent manner. Using alanine scanning mutagenesis of amino acids in the catalytic active site, we pinpoint particular residues in QueE that contribute distinctly to each of its functions - Q biosynthesis or regulation of cell division, establishing QueE as a moonlighting protein. We further show that QueE orthologs from enterobacteria like Salmonella typhimurium and Klebsiella pneumoniae also cause filamentation in these organisms, but the more distant counterparts from Pseudomonas aeruginosa and Bacillus subtilis lack this ability. By comparative analysis of E. coli QueE with distant orthologs, we elucidate a unique region in this protein that is responsible for QueEs secondary function as a cell division regulator. A dual-function protein like QueE is an exception to the conventional model of one gene, one enzyme, one function, which has divergent roles across a range of fundamental cellular processes including RNA modification and translation to cell division and stress response.
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11
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Adeleye SA, Yadavalli SS. Queuosine biosynthetic enzyme, QueE moonlights as a cell division regulator. PLoS Genet 2024; 20:e1011287. [PMID: 38768229 PMCID: PMC11142719 DOI: 10.1371/journal.pgen.1011287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 05/31/2024] [Accepted: 05/03/2024] [Indexed: 05/22/2024] Open
Abstract
In many organisms, stress responses to adverse environments can trigger secondary functions of certain proteins by altering protein levels, localization, activity, or interaction partners. Escherichia coli cells respond to the presence of specific cationic antimicrobial peptides by strongly activating the PhoQ/PhoP two-component signaling system, which regulates genes important for growth under this stress. As part of this pathway, a biosynthetic enzyme called QueE, which catalyzes a step in the formation of queuosine (Q) tRNA modification is upregulated. When cellular QueE levels are high, it co-localizes with the central cell division protein FtsZ at the septal site, blocking division and resulting in filamentous growth. Here we show that QueE affects cell size in a dose-dependent manner. Using alanine scanning mutagenesis of amino acids in the catalytic active site, we pinpoint residues in QueE that contribute distinctly to each of its functions-Q biosynthesis or regulation of cell division, establishing QueE as a moonlighting protein. We further show that QueE orthologs from enterobacteria like Salmonella typhimurium and Klebsiella pneumoniae also cause filamentation in these organisms, but the more distant counterparts from Pseudomonas aeruginosa and Bacillus subtilis lack this ability. By comparative analysis of E. coli QueE with distant orthologs, we elucidate a unique region in this protein that is responsible for QueE's secondary function as a cell division regulator. A dual-function protein like QueE is an exception to the conventional model of "one gene, one enzyme, one function", which has divergent roles across a range of fundamental cellular processes including RNA modification and translation to cell division and stress response.
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Affiliation(s)
- Samuel A. Adeleye
- Waksman Institute of Microbiology and Department of Genetics, Rutgers University, Piscataway New Jersey, United States of America
| | - Srujana S. Yadavalli
- Waksman Institute of Microbiology and Department of Genetics, Rutgers University, Piscataway New Jersey, United States of America
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12
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Dang C, Morrissey EM. The size and diversity of microbes determine carbon use efficiency in soil. Environ Microbiol 2024; 26:e16633. [PMID: 38733078 DOI: 10.1111/1462-2920.16633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 04/24/2024] [Indexed: 05/13/2024]
Abstract
Soil is home to a multitude of microorganisms from all three domains of life. These organisms and their interactions are crucial in driving the cycling of soil carbon. One key indicator of this process is Microbial Carbon Use Efficiency (CUE), which shows how microbes influence soil carbon storage through their biomass production. Although CUE varies among different microorganisms, there have been few studies that directly examine how biotic factors influence CUE. One such factor could be body size, which can impact microbial growth rates and interactions in soil, thereby influencing CUE. Despite this, evidence demonstrating a direct causal connection between microbial biodiversity and CUE is still scarce. To address these knowledge gaps, we conducted an experiment where we manipulated microbial body size and biodiversity through size-selective filtering. Our findings show that manipulating the structure of the microbial community can reduce CUE by approximately 65%. When we restricted the maximum body size of the microbial community, we observed a reduction in bacterial diversity and functional potential, which in turn lowered the community's CUE. Interestingly, when we included large body size micro-eukarya in the soil, it shifted the soil carbon cycling, increasing CUE by approximately 50% and the soil carbon to nitrogen ratio by about 25%. Our metrics of microbial diversity and community structure were able to explain 36%-50% of the variation in CUE. This highlights the importance of microbial traits, community structure and trophic interactions in mediating soil carbon cycling.
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Affiliation(s)
- Chansotheary Dang
- Division of Plant and Soil Sciences, West Virginia University, Morgantown, West Virginia, USA
| | - Ember M Morrissey
- Division of Plant and Soil Sciences, West Virginia University, Morgantown, West Virginia, USA
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13
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Thweatt JL, Harman CE, Araújo MN, Marlow JJ, Oliver GC, Sabuda MC, Sevgen S, Wilpiszeki RL. Chapter 6: The Breadth and Limits of Life on Earth. ASTROBIOLOGY 2024; 24:S124-S142. [PMID: 38498824 DOI: 10.1089/ast.2021.0131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/20/2024]
Abstract
Scientific ideas about the potential existence of life elsewhere in the universe are predominantly informed by knowledge about life on Earth. Over the past ∼4 billion years, life on Earth has evolved into millions of unique species. Life now inhabits nearly every environmental niche on Earth that has been explored. Despite the wide variety of species and diverse biochemistry of modern life, many features, such as energy production mechanisms and nutrient requirements, are conserved across the Tree of Life. Such conserved features help define the operational parameters required by life and therefore help direct the exploration and evaluation of habitability in extraterrestrial environments. As new diversity in the Tree of Life continues to expand, so do the known limits of life on Earth and the range of environments considered habitable elsewhere. The metabolic processes used by organisms living on the edge of habitability provide insights into the types of environments that would be most suitable to hosting extraterrestrial life, crucial for planning and developing future astrobiology missions. This chapter will introduce readers to the breadth and limits of life on Earth and show how the study of life at the extremes can inform the broader field of astrobiology.
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Affiliation(s)
- Jennifer L Thweatt
- Department of Biochemistry and Molecular Biology, Penn State University, University Park, Pennsylvania, USA. (Former)
| | - C E Harman
- Planetary Systems Branch, NASA Ames Research Center, Moffett Field, California, USA
| | - M N Araújo
- Biochemistry Department, University of São Paulo, São Carlos, Brazil
| | - Jeffrey J Marlow
- Department of Biology, Boston University, Boston, Massachusetts, USA
| | - Gina C Oliver
- Department of Geology, San Bernardino Valley College, San Bernardino, California, USA
| | - Mary C Sabuda
- Department of Earth and Environmental Sciences, University of Minnesota-Twin Cities, Minneapolis, Minnesota, USA
- Biotechnology Institute, University of Minnesota-Twin Cities, St. Paul, Minnesota, USA
| | - Serhat Sevgen
- Institute of Marine Sciences, Middle East Technical University, Erdemli, Mersin, Turkey
- Blue Marble Space Institute of Science, Seattle, Washington, USA
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14
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Pan B, El-Moghazy AY, Norwood M, Nitin N, Sun G. Rapid and Ultrasensitive Colorimetric Biosensors for Onsite Detection of Escherichia coli O157:H7 in Fluids. ACS Sens 2024; 9:912-922. [PMID: 38320289 PMCID: PMC10897931 DOI: 10.1021/acssensors.3c02339] [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: 11/02/2023] [Revised: 01/18/2024] [Accepted: 01/24/2024] [Indexed: 02/08/2024]
Abstract
This study presents a breakthrough in the field of onsite bacterial detection, offering an innovative, rapid, and ultrasensitive colorimetric biosensor for the detection of Escherichia coli (E. coli) O157:H7, using chemically modified melamine foam (MF). Different from conventional platforms, such as 96-well plates and fiber-based membranes, the modified MF features a macroporous reticulated three-dimensional (3D) framework structure, allowing fast and free movement of large biomolecules and bacteria cells through the MF structure in every direction and ensuring good accessibility of entire active binding sites of the framework structure with the target bacteria, which significantly increased sensitive and volume-responsive detection of whole-cell bacteria. The biosensing platform requires less than 1.5 h to complete the quantitative detection with a sensitivity of 10 cfu/mL, discernible by the naked eye, and an enhanced sensitivity of 5 cfu/mL with the help of a smartphone. Following a short enrichment period of 1 h, the sensitivity was further amplified to 2 cfu/mL. The biosensor material is volume responsive, making the biosensing platform sensitivity increase as the volume of the sample increases, and is highly suitable for testing large-volume fluid samples. This novel material paves the way for the development of volume-flexible biosensing platforms for the record-fast, onsite, selective, and ultrasensitive detection of various pathogenic bacteria in real-world applications.
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Affiliation(s)
- Bofeng Pan
- Biological
and Agricultural Engineering, University
of California, Davis, California 95616, United States
| | - Ahmed Y. El-Moghazy
- Department
of Food Science and Technology, University
of California, Davis, California 95616, United States
| | - Makela Norwood
- Biological
and Agricultural Engineering, University
of California, Davis, California 95616, United States
| | - Nitin Nitin
- Biological
and Agricultural Engineering, University
of California, Davis, California 95616, United States
- Department
of Food Science and Technology, University
of California, Davis, California 95616, United States
| | - Gang Sun
- Biological
and Agricultural Engineering, University
of California, Davis, California 95616, United States
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15
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Soni J, Sinha S, Pandey R. Understanding bacterial pathogenicity: a closer look at the journey of harmful microbes. Front Microbiol 2024; 15:1370818. [PMID: 38444801 PMCID: PMC10912505 DOI: 10.3389/fmicb.2024.1370818] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Accepted: 02/05/2024] [Indexed: 03/07/2024] Open
Abstract
Bacteria are the most prevalent form of microorganisms and are classified into two categories based on their mode of existence: intracellular and extracellular. While most bacteria are beneficial to human health, others are pathogenic and can cause mild to severe infections. These bacteria use various mechanisms to evade host immunity and cause diseases in humans. The susceptibility of a host to bacterial infection depends on the effectiveness of the immune system, overall health, and genetic factors. Malnutrition, chronic illnesses, and age-related vulnerabilities are the additional confounders to disease severity phenotypes. The impact of bacterial pathogens on public health includes the transmission of these pathogens from healthcare facilities, which contributes to increased morbidity and mortality. To identify the most significant threats to public health, it is crucial to understand the global burden of common bacterial pathogens and their pathogenicity. This knowledge is required to improve immunization rates, improve the effectiveness of vaccines, and consider the impact of antimicrobial resistance when assessing the situation. Many bacteria have developed antimicrobial resistance, which has significant implications for infectious diseases and favors the survival of resilient microorganisms. This review emphasizes the significance of understanding the bacterial pathogens that cause this health threat on a global scale.
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Affiliation(s)
- Jyoti Soni
- Division of Immunology and Infectious Disease Biology, Integrative Genomics of Host Pathogen Laboratory, Council of Scientific & Industrial Research-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy of Scientific and Innovative Research, Ghaziabad, India
| | - Sristi Sinha
- Division of Immunology and Infectious Disease Biology, Integrative Genomics of Host Pathogen Laboratory, Council of Scientific & Industrial Research-Institute of Genomics and Integrative Biology, New Delhi, India
- School of Biosciences and Technology, Vellore Institute of Technology University, Vellore, India
| | - Rajesh Pandey
- Division of Immunology and Infectious Disease Biology, Integrative Genomics of Host Pathogen Laboratory, Council of Scientific & Industrial Research-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy of Scientific and Innovative Research, Ghaziabad, India
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16
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Cabral LDS, Weimer PJ. Megasphaera elsdenii: Its Role in Ruminant Nutrition and Its Potential Industrial Application for Organic Acid Biosynthesis. Microorganisms 2024; 12:219. [PMID: 38276203 PMCID: PMC10819428 DOI: 10.3390/microorganisms12010219] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 01/15/2024] [Accepted: 01/19/2024] [Indexed: 01/27/2024] Open
Abstract
The Gram-negative, strictly anaerobic bacterium Megasphaera elsdenii was first isolated from the rumen in 1953 and is common in the mammalian gastrointestinal tract. Its ability to use either lactate or glucose as its major energy sources for growth has been well documented, although it can also ferment amino acids into ammonia and branched-chain fatty acids, which are growth factors for other bacteria. The ruminal abundance of M. elsdenii usually increases in animals fed grain-based diets due to its ability to use lactate (the product of rapid ruminal sugar fermentation), especially at a low ruminal pH (<5.5). M. elsdenii has been proposed as a potential dietary probiotic to prevent ruminal acidosis in feedlot cattle and high-producing dairy cows. However, this bacterium has also been associated with milk fat depression (MFD) in dairy cows, although proving a causative role has remained elusive. This review summarizes the unique physiology of this intriguing bacterium and its functional role in the ruminal community as well as its role in the health and productivity of the host animal. In addition to its effects in the rumen, the ability of M. elsdenii to produce C2-C7 carboxylic acids-potential precursors for industrial fuel and chemical production-is examined.
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Affiliation(s)
- Luciano da Silva Cabral
- Department of Animal Science and Rural Extension, Agronomy and Animal Science School, Federal University of Mato Grosso, Cuiabá 780600-900, Mato Grosso, Brazil;
| | - Paul J. Weimer
- Department of Bacteriology, University of Wisconsin, Madison, WI 53706, USA
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17
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Tyumina E, Bazhutin G, Kostrikina N, Sorokin V, Mulyukin A, Ivshina I. Phenotypic and metabolic adaptations of Rhodococcus cerastii strain IEGM 1243 to separate and combined effects of diclofenac and ibuprofen. Front Microbiol 2023; 14:1275553. [PMID: 38125575 PMCID: PMC10730942 DOI: 10.3389/fmicb.2023.1275553] [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: 08/10/2023] [Accepted: 11/21/2023] [Indexed: 12/23/2023] Open
Abstract
Introduction The increasing use of non-steroidal anti-inflammatory drugs (NSAIDs) has raised concerns regarding their environmental impact. To address this, understanding the effects of NSAIDs on bacteria is crucial for bioremediation efforts in pharmaceutical-contaminated environments. The primary challenge in breaking down persistent compounds lies not in the biochemical pathways but in capacity of bacteria to surmount stressors. Methods In this study, we examined the biodegradative activity, morphological and physiological changes, and ultrastructural adaptations of Rhodococcus cerastii strain IEGM 1243 when exposed to ibuprofen, diclofenac, and their mixture. Results and Discussion Our findings revealed that R. cerastii IEGM 1243 exhibited moderate biodegradative activity towards the tested NSAIDs. Cellular respiration assay showed higher metabolic activity in the presence of NSAIDs, indicating their influence on bacterial metabolism. Furthermore, catalase activity in R. cerastii IEGM 1243 exposed to NSAIDs showed an initial decrease followed by fluctuations, with the most significant changes observed in the presence of DCF and the NSAID mixture, likely influenced by bacterial growth phases, active NSAID degradation, and the formation of multicellular aggregates, suggesting potential intercellular synergy and task distribution within the bacterial community. Morphometric analysis demonstrated alterations in size, shape, and surface roughness of cells exposed to NSAIDs, with a decrease in surface area and volume, and an increase in surface area-to-volume ratio (SA/V). Moreover, for the first time, transmission electron microscopy confirmed the presence of lipid inclusions, polyphosphates, and intracellular membrane-like structures in the ibuprofen-treated cells. Conclusion These results provide valuable insights into the adaptive responses of R. cerastii IEGM 1243 to NSAIDs, shedding light on the possible interaction between bacteria and pharmaceutical compounds in the environment.
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Affiliation(s)
- Elena Tyumina
- Perm Federal Research Center, Ural Branch of the Russian Academy of Sciences, Institute of Ecology and Genetics of Microorganisms, Perm, Russia
- Department of Microbiology and Immunology, Perm State University, Perm, Russia
| | - Grigory Bazhutin
- Perm Federal Research Center, Ural Branch of the Russian Academy of Sciences, Institute of Ecology and Genetics of Microorganisms, Perm, Russia
- Department of Microbiology and Immunology, Perm State University, Perm, Russia
| | - Nadezhda Kostrikina
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Vladimir Sorokin
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Andrey Mulyukin
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Irina Ivshina
- Perm Federal Research Center, Ural Branch of the Russian Academy of Sciences, Institute of Ecology and Genetics of Microorganisms, Perm, Russia
- Department of Microbiology and Immunology, Perm State University, Perm, Russia
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18
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Roll W, Faust A, Hermann S, Schäfers M. Infection Imaging: Focus on New Tracers? J Nucl Med 2023; 64:59S-67S. [PMID: 37918846 DOI: 10.2967/jnumed.122.264869] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 05/31/2023] [Indexed: 11/04/2023] Open
Abstract
Infections account for relevant morbidity and mortality, especially if the cardiovascular system is affected. Clinical manifestations are often unspecific, resulting in a challenging diagnostic work-up. The use of molecular imaging methods, namely [18F]FDG PET and leukocyte scintigraphy, is increasingly recognized in recently published international guidelines. However, these 2 established methods focus on the host's immune response to the pathogen and are therefore virtually unable to differentiate infection from inflammation. Targeting the microorganism responsible for the infection directly with novel imaging agents is a promising strategy to overcome these limitations. In this review, we discuss clinically approved [18F]FDG PET with its advantages and limitations in cardiovascular infections, followed by new PET-based approaches for the detection of cardiovascular infections by bacteria-specific molecular imaging methods. A multitude of different targeting options has already been preclinically evaluated, but most still lack clinical translation. We give an overview not only on promising tracer candidates for noninvasive molecular imaging of infections but also on issues hampering clinical translation.
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Affiliation(s)
- Wolfgang Roll
- Department of Nuclear Medicine, University Hospital Münster, Münster, Germany; and
| | - Andreas Faust
- Department of Nuclear Medicine, University Hospital Münster, Münster, Germany; and
- European Institute for Molecular Imaging, University of Münster, Münster, Germany
| | - Sven Hermann
- European Institute for Molecular Imaging, University of Münster, Münster, Germany
| | - Michael Schäfers
- Department of Nuclear Medicine, University Hospital Münster, Münster, Germany; and
- European Institute for Molecular Imaging, University of Münster, Münster, Germany
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19
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Feng J, Zheng Y, Ma W, Ihsan A, Hao H, Cheng G, Wang X. Multitarget antibacterial drugs: An effective strategy to combat bacterial resistance. Pharmacol Ther 2023; 252:108550. [PMID: 39492518 DOI: 10.1016/j.pharmthera.2023.108550] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 10/19/2023] [Accepted: 10/23/2023] [Indexed: 11/05/2024]
Abstract
The rise of antibiotic resistance and the decrease in the discovery of new antibiotics have caused a global health crisis. Of particular concern is the fact that despite efforts to develop new antibiotics, drug discovery is unable to keep up with the rapid development of resistance. This ongoing crisis highlights the fact that single-target drugs may not always exhibit satisfactory therapeutic effects and are prone to target mutations and resistance due to the complexity of bacterial mechanisms. Retrospective studies have shown that most successful antibiotics have multiple targets. Compared with single-target drugs, successfully designed multitarget drugs can simultaneously regulate multiple targets to reduce resistance caused by single-target mutations or expression changes. In addition to a lower risk of drug-drug interactions, multitarget drugs show superior pharmacokinetics and higher patient compliance compared with combination therapies. Therefore, to reduce resistance, many efforts have been made to discover and design multitarget drugs with different chemical structures and functions. Although there have been numerous studies on how to develop drugs and slow down the development of drug resistance, the reduction of bacterial resistance by multitarget antibacterial drugs has not received widespread attention and is rarely mentioned in the peer-reviewed literature. This review summarises the development of antibiotic resistance and the mechanisms proposed for its emergence, examines the potential of multitarget drugs as an effective strategy to slow the development of resistance, and discusses the rationale for multitarget drug therapy. We also describe multitarget antibacterial compounds with the potential to reduce drug resistance and the available strategies to develop multitarget drugs.
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Affiliation(s)
- Jin Feng
- National Reference Laboratory of Veterinary Drug Residues (HZAU) and MAO Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Youle Zheng
- MAO Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Wanqing Ma
- MAO Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Awais Ihsan
- Department of Biosciences, COMSATS University Islamabad, Sahiwal Campus, Islamabad 45550, Pakistan
| | - Haihong Hao
- National Reference Laboratory of Veterinary Drug Residues (HZAU) and MAO Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan, Hubei 430070, China; MAO Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Guyue Cheng
- National Reference Laboratory of Veterinary Drug Residues (HZAU) and MAO Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan, Hubei 430070, China; MAO Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Xu Wang
- National Reference Laboratory of Veterinary Drug Residues (HZAU) and MAO Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan, Hubei 430070, China; MAO Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan, Hubei 430070, China.
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20
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Amieva-Balmori M, García-Mazcorro JF, Martínez-Conejo A, Hernández-Ramírez GA, García-Zermeño KR, Rodríguez-Aguilera O, Aja-Cadena M, Barradas-Cortés M, Quigley EMM, Remes-Troche JM. Fecal bacterial microbiota in constipated patients before and after eight weeks of daily Bifidobacterium infantis 35624 administration. REVISTA DE GASTROENTEROLOGIA DE MEXICO (ENGLISH) 2023; 88:369-380. [PMID: 35810091 DOI: 10.1016/j.rgmxen.2022.06.014] [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: 01/17/2022] [Accepted: 04/04/2022] [Indexed: 10/17/2022]
Abstract
INTRODUCTION AND AIM In recent years, probiotics have been used in functional gastrointestinal disorders, including chronic constipation (CC). The effect of Bifidobacterium infantis strain 35624 on the gut microbiota of CC patients has not been previously studied. Our aim was to analyze the fecal microbiota of constipated patients, before and after consuming a single-strain probiotic (B. infantis strain 35624). MATERIALS AND METHODS We used 16S rRNA gene high-throughput sequencing to analyze the fecal microbiota of female patients (n=13) with CC. Patients were instructed to ingest one capsule of Alflorex® (containing 1×109 CFUs/g B. infantis strain 35624) daily for eight weeks. Fecal samples were obtained at the baseline and end (final) of probiotic administration. RESULTS Alpha diversity metrics did not differ between the baseline and final periods. The butyrate producer, Oscillospira, was the taxon most strongly correlated with amplicon sequence variants (R2=0.55, p<0.0001). Except for a few bacterial taxa, there were no significant differences in relative abundance between the baseline and final periods. Beta-diversity measures also showed limited evidence for the differences between the two time periods. CONCLUSIONS The results suggest that the fecal bacterial microbiota remains stable in constipated women consuming a single-strain probiotic. Those findings may be helpful in better understanding probiotic functioning in patients with digestive disorders.
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Affiliation(s)
- M Amieva-Balmori
- Laboratorio de Fisiología Digestiva y Motilidad Gastrointestinal, Instituto de Investigaciones Medico-Biológicas, Universidad Veracruzana, Veracruz, México
| | - J F García-Mazcorro
- Laboratorio de Fisiología Digestiva y Motilidad Gastrointestinal, Instituto de Investigaciones Medico-Biológicas, Universidad Veracruzana, Veracruz, México
| | - A Martínez-Conejo
- Laboratorio de Fisiología Digestiva y Motilidad Gastrointestinal, Instituto de Investigaciones Medico-Biológicas, Universidad Veracruzana, Veracruz, México
| | - G A Hernández-Ramírez
- Laboratorio de Fisiología Digestiva y Motilidad Gastrointestinal, Instituto de Investigaciones Medico-Biológicas, Universidad Veracruzana, Veracruz, México
| | - K R García-Zermeño
- Laboratorio de Fisiología Digestiva y Motilidad Gastrointestinal, Instituto de Investigaciones Medico-Biológicas, Universidad Veracruzana, Veracruz, México
| | - O Rodríguez-Aguilera
- Laboratorio de Fisiología Digestiva y Motilidad Gastrointestinal, Instituto de Investigaciones Medico-Biológicas, Universidad Veracruzana, Veracruz, México
| | - M Aja-Cadena
- Laboratorio de Fisiología Digestiva y Motilidad Gastrointestinal, Instituto de Investigaciones Medico-Biológicas, Universidad Veracruzana, Veracruz, México
| | - M Barradas-Cortés
- Laboratorio de Fisiología Digestiva y Motilidad Gastrointestinal, Instituto de Investigaciones Medico-Biológicas, Universidad Veracruzana, Veracruz, México
| | - E M M Quigley
- Lynda K and David M Underwood Center for Digestive Disorders, Houston Methodist Hospital and Weill Cornell Medical College, Houston, TX, USA
| | - J M Remes-Troche
- Laboratorio de Fisiología Digestiva y Motilidad Gastrointestinal, Instituto de Investigaciones Medico-Biológicas, Universidad Veracruzana, Veracruz, México.
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21
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Schirmer M, Dusny C. Microbial single-cell mass spectrometry: status, challenges, and prospects. Curr Opin Biotechnol 2023; 83:102977. [PMID: 37515936 DOI: 10.1016/j.copbio.2023.102977] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 07/04/2023] [Accepted: 07/05/2023] [Indexed: 07/31/2023]
Abstract
Single-cell analysis uncovers phenotypic differences between cells in a population and dissects their individual physiological states and differences on all omics levels from genome to phenome. Spectrometric observation allows label-free analysis of the metabolome and proteome of individual cells, but is still mainly limited to the analysis of mammalian single cells. Recent progress in mass spectrometry approaches now enables the analysis of microbial single cells - mainly by miniaturizing cell handling, incubation, and improving chip-coupling concepts for analyte ionization by interfacing microfluidic chips and mass spectrometers. This review aims at distilling the enabling principles behind microbial single-cell mass spectrometry and puts them into perspective for the future of the field.
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Affiliation(s)
- Martin Schirmer
- Department of Solar Materials - Microscale Analysis and Engineering, Helmholtz-Centre for Environmental Research - UFZ Leipzig, Leizpig, Germany
| | - Christian Dusny
- Department of Solar Materials - Microscale Analysis and Engineering, Helmholtz-Centre for Environmental Research - UFZ Leipzig, Leizpig, Germany.
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22
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Szymczak B. Phenotypic and Genotypic Characteristics of Non-Hemolytic L. monocytogenes Isolated from Food and Processing Environments. Foods 2023; 12:3630. [PMID: 37835283 PMCID: PMC10572806 DOI: 10.3390/foods12193630] [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: 09/07/2023] [Revised: 09/25/2023] [Accepted: 09/27/2023] [Indexed: 10/15/2023] Open
Abstract
Increasingly, Listeria monocytogenes (LM) with atypical phenotypic and genotypic characteristics are being isolated from food, causing problems with their classification and testing. From 2495 soil, food, and swab samples from the food industry, 262 LM isolates were found. A total of 30 isolates were isolated, mainly from soil and plant food, and were classified as atypical LM (aLM) because they lacked the ability to move (30/11.4%) and perform hemolysis (25/9.5%). The isolation environment affected aLM incidence, cell size, sugar fermentation capacity, antibiotic sensitivity, and the number of virulence genes. Therefore, despite several characteristics differentiating all aLMs/non-hemolytic isolates from reference LMs, the remaining phenotypic characteristics were specific to each aLM isolate (like a fingerprint). The aLM/non-hemolytic isolates, particularly those from the soil and meat industries, showed more variability in their sugar fermentation capacity and were less sensitive to antibiotics than LMs. As many as 11 (36.7%) aLM isolates had resistance to four different antibiotics or simultaneously to two antibiotics. The aLM isolates possessed 3-7 of the 12 virulence genes: prfA and hly in all aLMs, while iap was not present. Only five (16.7%) isolates were classified into serogroups 1/2c-3c or 4a-4c. The aLM/non-hemolytic isolates differed by many traits from L. immobilis and atypical L. innocua. The reference method of reviving and isolating LM required optimization of aLM. Statistical analyses of clustering, correlation, and PCA showed similarities and differences between LM and aLM/non-hemolytic isolates due to individual phenotypic traits and genes. Correlations were found between biochemical traits, antibiotic resistance, and virulence genes. The increase in the incidence of atypical non-hemolytic LM may pose a risk to humans, as they may not be detected by ISO methods and have greater antibiotic resistance than LM. aLM from LM can be distinguished based on lack of hemolysis, motility, growth at 4 °C, ability to ferment D-arabitol, and lack of six specific genes.
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Affiliation(s)
- Barbara Szymczak
- Department of Applied Microbiology and Human Nutrition Physiology, Faculty of Food Science and Fisheries, West Pomeranian University of Technology, Papieża Pawła VI 3, 71-459 Szczecin, Poland
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23
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Ionescu D, Volland JM, Contarini PE, Gros O. Genomic Mysteries of Giant Bacteria: Insights and Implications. Genome Biol Evol 2023; 15:evad163. [PMID: 37708391 PMCID: PMC10519445 DOI: 10.1093/gbe/evad163] [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: 03/27/2023] [Revised: 08/18/2023] [Accepted: 09/01/2023] [Indexed: 09/16/2023] Open
Abstract
Bacteria and Archaea are traditionally regarded as organisms with a simple morphology constrained to a size of 2-3 µm. Nevertheless, the history of microbial research is rich in the description of giant bacteria exceeding tens and even hundreds of micrometers in length or diameter already from its early days, for example, Beggiatoa spp., to the present, for example, Candidatus Thiomargarita magnifica. While some of these giants are still being studied, some were lost to science, with merely drawings and photomicrographs as evidence for their existence. The physiology and biogeochemical role of giant bacteria have been studied, with a large focus on those involved in the sulfur cycle. With the onset of the genomic era, no special emphasis has been given to this group, in an attempt to gain a novel, evolutionary, and molecular understanding of the phenomenon of bacterial gigantism. The few existing genomic studies reveal a mysterious world of hyperpolyploid bacteria with hundreds to hundreds of thousands of chromosomes that are, in some cases, identical and in others, extremely different. These studies on giant bacteria reveal novel organelles, cellular compartmentalization, and novel mechanisms to combat the accumulation of deleterious mutations in polyploid bacteria. In this perspective paper, we provide a brief overview of what is known about the genomics of giant bacteria and build on that to highlight a few burning questions that await to be addressed.
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Affiliation(s)
- Danny Ionescu
- Department of Plankton and Microbial Ecology, Leibniz Institute of Freshwater Ecology and Inland Fisheries, Neuglobsow, Germany
| | - Jean-Marie Volland
- Laboratory for Research in Complex Systems, Menlo Park, California, USA
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Paul-Emile Contarini
- Laboratory for Research in Complex Systems, Menlo Park, California, USA
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d’Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Pointe-à-Pitre, France
| | - Olivier Gros
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d’Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Pointe-à-Pitre, France
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24
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Lin TY, Liu WT. Validation of 16S rRNA gene sequencing and metagenomics for evaluating microbial immigration in a methanogenic bioreactor. WATER RESEARCH 2023; 243:120358. [PMID: 37481999 DOI: 10.1016/j.watres.2023.120358] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Revised: 07/09/2023] [Accepted: 07/14/2023] [Indexed: 07/25/2023]
Abstract
To quantitatively evaluate the impact of microbial immigration from an upstream community on the microbial assembly of a downstream community, an ecological genomics (ecogenomics)-based mass balance (EGMB) model coupled with 16S rRNA gene sequencing was previously developed. In this study, a mock community was used to further validate the EGMB models and demonstrate the feasibility of using metagenome-based EGMB model to reveal both microbial activity and function. The mock community consisting of Aeromonas, Escherichia, and Pseudomonas was fed into a lab-scale methanogenic bioreactor together with dissolved organic substrate. Using qPCR, 16S rRNA gene, 16S rRNA gene copy number normalization (GCN), and metagenome, results showed highly comparable community profiles in the feed. In the bioreactor, Aeromonas and Pseudomonas exhibited negative growth rates throughout the experiment by all approaches. Escherichia's growth rate was negative by most biomarkers but was slightly positive by 16S rRNA gene. Still, all approaches showed a decreasing trend toward negative in the growth rate of Escherichia as reactor operation time increased. Uncultivated populations of phyla Desulfobacterota, Chloroflexi, Actinobacteriota, and Spirochaetota were observed to increase in abundance, suggesting their contribution in degrading the feed biomass. Based on metabolic reconstruction of metagenomes, these populations possessed functions of hydrolysis, fermentation, fatty acid degradation, or acetate oxidation. Overall results supported the application of both 16S rRNA gene- and metagenome-based EGMB models to measure the growth rate of microbes in the bioreactor, and the latter had advantage in providing insights into the microbial functions of uncultivated populations.
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Affiliation(s)
- Tzu-Yu Lin
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Wen-Tso Liu
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
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25
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Mermans F, Mattelin V, Van den Eeckhoudt R, García-Timermans C, Van Landuyt J, Guo Y, Taurino I, Tavernier F, Kraft M, Khan H, Boon N. Opportunities in optical and electrical single-cell technologies to study microbial ecosystems. Front Microbiol 2023; 14:1233705. [PMID: 37692384 PMCID: PMC10486927 DOI: 10.3389/fmicb.2023.1233705] [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] [Received: 06/02/2023] [Accepted: 08/03/2023] [Indexed: 09/12/2023] Open
Abstract
New techniques are revolutionizing single-cell research, allowing us to study microbes at unprecedented scales and in unparalleled depth. This review highlights the state-of-the-art technologies in single-cell analysis in microbial ecology applications, with particular attention to both optical tools, i.e., specialized use of flow cytometry and Raman spectroscopy and emerging electrical techniques. The objectives of this review include showcasing the diversity of single-cell optical approaches for studying microbiological phenomena, highlighting successful applications in understanding microbial systems, discussing emerging techniques, and encouraging the combination of established and novel approaches to address research questions. The review aims to answer key questions such as how single-cell approaches have advanced our understanding of individual and interacting cells, how they have been used to study uncultured microbes, which new analysis tools will become widespread, and how they contribute to our knowledge of ecological interactions.
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Affiliation(s)
- Fabian Mermans
- Center for Microbial Ecology and Technology (CMET), Department of Biotechnology, Ghent University, Ghent, Belgium
- Department of Oral Health Sciences, KU Leuven, Leuven, Belgium
| | - Valérie Mattelin
- Center for Microbial Ecology and Technology (CMET), Department of Biotechnology, Ghent University, Ghent, Belgium
| | - Ruben Van den Eeckhoudt
- Micro- and Nanosystems (MNS), Department of Electrical Engineering (ESAT), KU Leuven, Leuven, Belgium
| | - Cristina García-Timermans
- Center for Microbial Ecology and Technology (CMET), Department of Biotechnology, Ghent University, Ghent, Belgium
| | - Josefien Van Landuyt
- Center for Microbial Ecology and Technology (CMET), Department of Biotechnology, Ghent University, Ghent, Belgium
| | - Yuting Guo
- Center for Microbial Ecology and Technology (CMET), Department of Biotechnology, Ghent University, Ghent, Belgium
| | - Irene Taurino
- Micro- and Nanosystems (MNS), Department of Electrical Engineering (ESAT), KU Leuven, Leuven, Belgium
- Semiconductor Physics, Department of Physics and Astronomy, KU Leuven, Leuven, Belgium
| | - Filip Tavernier
- MICAS, Department of Electrical Engineering (ESAT), KU Leuven, Leuven, Belgium
| | - Michael Kraft
- Micro- and Nanosystems (MNS), Department of Electrical Engineering (ESAT), KU Leuven, Leuven, Belgium
- Leuven Institute of Micro- and Nanoscale Integration (LIMNI), KU Leuven, Leuven, Belgium
| | - Hira Khan
- Center for Microbial Ecology and Technology (CMET), Department of Biotechnology, Ghent University, Ghent, Belgium
| | - Nico Boon
- Center for Microbial Ecology and Technology (CMET), Department of Biotechnology, Ghent University, Ghent, Belgium
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26
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Truong VK, Hayles A, Bright R, Luu TQ, Dickey MD, Kalantar-Zadeh K, Vasilev K. Gallium Liquid Metal: Nanotoolbox for Antimicrobial Applications. ACS NANO 2023; 17:14406-14423. [PMID: 37506260 DOI: 10.1021/acsnano.3c06486] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2023]
Abstract
The proliferation of drug resistance in microbial pathogens poses a significant threat to human health. Hence, treatment measures are essential to surmount this growing problem. In this context, liquid metal nanoparticles are promising. Gallium, a post-transition metal notable for being a liquid at physiological temperature, has drawn attention for its distinctive properties, high antimicrobial efficacy, and low toxicity. Moreover, gallium nanoparticles demonstrate anti-inflammatory properties in immune cells. Gallium can alloy with other metals and be prepared in various composites to modify and tailor its characteristics and functionality. More importantly, the bactericidal mechanism of gallium liquid metal could sidestep the threat of emerging drug resistance mechanisms. Building on this rationale, gallium-based liquid metal nanoparticles can enable impactful and innovative strategic pathways in the battle against antimicrobial resistance. This review outlines the characteristics of gallium-based liquid metals at the nanoscale and their corresponding antimicrobial mechanisms to provide a comprehensive yet succinct overview of their current antimicrobial applications. In addition, challenges and opportunities that require further research efforts have been identified and discussed.
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Affiliation(s)
- Vi Khanh Truong
- Biomedical Nanoengineering Laboratory, College of Medicine and Public Health, Flinders University, Bedford Park, South Australia 5042, Australia
| | - Andrew Hayles
- Biomedical Nanoengineering Laboratory, College of Medicine and Public Health, Flinders University, Bedford Park, South Australia 5042, Australia
| | - Richard Bright
- Biomedical Nanoengineering Laboratory, College of Medicine and Public Health, Flinders University, Bedford Park, South Australia 5042, Australia
| | - Trong Quan Luu
- Biomedical Nanoengineering Laboratory, College of Medicine and Public Health, Flinders University, Bedford Park, South Australia 5042, Australia
| | - Michael D Dickey
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Kourosh Kalantar-Zadeh
- School of Chemical and Biomolecular Engineering, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Krasimir Vasilev
- Biomedical Nanoengineering Laboratory, College of Medicine and Public Health, Flinders University, Bedford Park, South Australia 5042, Australia
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27
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Parisi M, Lucidi M, Visca P, Cincotti G. Super-Resolution Optical Imaging of Bacterial Cells. IEEE JOURNAL OF SELECTED TOPICS IN QUANTUM ELECTRONICS 2023; 29:1-13. [DOI: 10.1109/jstqe.2022.3228121] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2025]
Affiliation(s)
- Miranda Parisi
- Engineering Department, University Roma Tre, Rome, Italy
| | | | - Paolo Visca
- Science Department, University Roma Tre, Rome, Italy
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28
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Hoang MN, Peterbauer C. Double-Labeling Method for Visualization and Quantification of Membrane-Associated Proteins in Lactococcus lactis. Int J Mol Sci 2023; 24:10586. [PMID: 37445764 DOI: 10.3390/ijms241310586] [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: 05/10/2023] [Revised: 06/21/2023] [Accepted: 06/21/2023] [Indexed: 07/15/2023] Open
Abstract
Lactococcus lactis displaying recombinant proteins on its surface can be used as a potential drug delivery vector in prophylactic medication and therapeutic treatments for many diseases. These applications enable live-cell mucosal and oral administration, providing painless, needle-free solutions and triggering robust immune response at the site of pathogen entry. Immunization requires quantitative control of antigens and, ideally, a complete understanding of the bacterial processing mechanism applied to the target proteins. In this study, we propose a double-labeling method based on a conjugated dye specific for a recombinantly introduced polyhistidine tag (to visualize surface-exposed proteins) and a membrane-permeable dye specific for a tetra-cysteine tag (to visualize cytoplasmic proteins), combined with a method to block the labeling of surface-exposed tetra-cysteine tags, to clearly obtain location-specific signals of the two dyes. This allows simultaneous detection and quantification of targeted proteins on the cell surface and in the cytoplasm. Using this method, we were able to detect full-length peptide chains for the model proteins HtrA and BmpA in L. lactis, which are associated with the cell membrane by two different attachment modes, and thus confirm that membrane-associated proteins in L. lactis are secreted using the Sec-dependent post-translational pathway. We were able to quantitatively follow cytoplasmic protein production and accumulation and subsequent export and surface attachment, which provides a convenient tool for monitoring these processes for cell surface display applications.
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Affiliation(s)
- Mai Ngoc Hoang
- Institute of Immunology, Department of Human Medicine, Carl von Ossietzky University of Oldenburg, 26129 Oldenburg, Germany
| | - Clemens Peterbauer
- Institute of Food Technology, Department of Food Science and Technology, University of Natural Resources and Life Sciences, 1190 Vienna, Austria
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29
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Asp ME, Thanh MTH, Dutta S, Comstock JA, Welch RD, Patteson AE. Mechanobiology as a tool for addressing the genotype-to-phenotype problem in microbiology. BIOPHYSICS REVIEWS 2023; 4:021304. [PMID: 38504926 PMCID: PMC10903382 DOI: 10.1063/5.0142121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 04/03/2023] [Indexed: 03/21/2024]
Abstract
The central hypothesis of the genotype-phenotype relationship is that the phenotype of a developing organism (i.e., its set of observable attributes) depends on its genome and the environment. However, as we learn more about the genetics and biochemistry of living systems, our understanding does not fully extend to the complex multiscale nature of how cells move, interact, and organize; this gap in understanding is referred to as the genotype-to-phenotype problem. The physics of soft matter sets the background on which living organisms evolved, and the cell environment is a strong determinant of cell phenotype. This inevitably leads to challenges as the full function of many genes, and the diversity of cellular behaviors cannot be assessed without wide screens of environmental conditions. Cellular mechanobiology is an emerging field that provides methodologies to understand how cells integrate chemical and physical environmental stress and signals, and how they are transduced to control cell function. Biofilm forming bacteria represent an attractive model because they are fast growing, genetically malleable and can display sophisticated self-organizing developmental behaviors similar to those found in higher organisms. Here, we propose mechanobiology as a new area of study in prokaryotic systems and describe its potential for unveiling new links between an organism's genome and phenome.
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30
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Padmakumar A, Pavani C, Eswar K, Kong L, Yang W, Gopalakrishnan S, Cahill DM, Rengan AK. Bacteria-Premised Nanobiopesticides for the Management of Phytopathogens and Pests. ACS AGRICULTURAL SCIENCE & TECHNOLOGY 2023; 3:370-388. [DOI: 10.1021/acsagscitech.3c00025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2025]
Affiliation(s)
- Ananya Padmakumar
- Department of Biomedical Engineering, Indian Institute of Technology Hyderabad, Telangana 502285, India
- Deakin University, Institute for Frontier Materials, Geelong, Victoria 3216, Australia
| | - Chowdary Pavani
- Department of Biomedical Engineering, Indian Institute of Technology Hyderabad, Telangana 502285, India
| | - Kalyani Eswar
- Department of Biomedical Engineering, Indian Institute of Technology Hyderabad, Telangana 502285, India
| | - Lingxue Kong
- Deakin University, Institute for Frontier Materials, Geelong, Victoria 3216, Australia
| | - Wenrong Yang
- School of Life and Environmental Sciences, Deakin University, 75 Pigdons Road, Waurn Ponds, Victoria 3216 Australia
| | | | - David Miles Cahill
- School of Life and Environmental Sciences, Deakin University, 75 Pigdons Road, Waurn Ponds, Victoria 3216 Australia
| | - Aravind Kumar Rengan
- Department of Biomedical Engineering, Indian Institute of Technology Hyderabad, Telangana 502285, India
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31
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Wang X, Zhang M, Zhu T, Wei Q, Liu G, Ding J. Flourishing Antibacterial Strategies for Osteomyelitis Therapy. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2206154. [PMID: 36717275 PMCID: PMC10104653 DOI: 10.1002/advs.202206154] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 12/05/2022] [Indexed: 06/18/2023]
Abstract
Osteomyelitis is a destructive disease of bone tissue caused by infection with pathogenic microorganisms. Because of the complex and long-term abnormal conditions, osteomyelitis is one of the refractory diseases in orthopedics. Currently, anti-infective therapy is the primary modality for osteomyelitis therapy in addition to thorough surgical debridement. However, bacterial resistance has gradually reduced the benefits of traditional antibiotics, and the development of advanced antibacterial agents has received growing attention. This review introduces the main targets of antibacterial agents for treating osteomyelitis, including bacterial cell wall, cell membrane, intracellular macromolecules, and bacterial energy metabolism, focuses on their mechanisms, and predicts prospects for clinical applications.
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Affiliation(s)
- Xukai Wang
- Department of Thoracic SurgeryChina‐Japan Union Hospital of Jilin University126 Xiantai StreetChangchun130033P. R. China
- Key Laboratory of Polymer EcomaterialsChangchun Institute of Applied ChemistryChinese Academy of Sciences5625 Renmin StreetChangchun130022P. R. China
| | - Mingran Zhang
- Department of Thoracic SurgeryChina‐Japan Union Hospital of Jilin University126 Xiantai StreetChangchun130033P. R. China
| | - Tongtong Zhu
- Department of Thoracic SurgeryChina‐Japan Union Hospital of Jilin University126 Xiantai StreetChangchun130033P. R. China
| | - Qiuhua Wei
- Department of Disinfection and Infection ControlChinese PLA Center for Disease Control and Prevention20 Dongda StreetBeijing100071P. R. China
| | - Guangyao Liu
- Department of Thoracic SurgeryChina‐Japan Union Hospital of Jilin University126 Xiantai StreetChangchun130033P. R. China
| | - Jianxun Ding
- Key Laboratory of Polymer EcomaterialsChangchun Institute of Applied ChemistryChinese Academy of Sciences5625 Renmin StreetChangchun130022P. R. China
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32
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Hammar R, Sellin ME, Artursson P. Epithelial and microbial determinants of colonic drug distribution. Eur J Pharm Sci 2023; 183:106389. [PMID: 36690119 DOI: 10.1016/j.ejps.2023.106389] [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: 10/31/2022] [Revised: 01/18/2023] [Accepted: 01/19/2023] [Indexed: 01/21/2023]
Abstract
A dynamic epithelium and a rich microbiota, separated by multi-layered mucus, make up the complex colonic cellular environment. Both cellular systems are characterized by high inter- and intraindividual differences, but their impact on drug distribution and efficacy remains incompletely understood. This research gap is pressing, as, e.g., inflammatory disorders of the colon are on the rise globally. In an effort to help close this gap, we provide considerations on determining colonic epithelial and microbial cellular parameters, and their impact on drug bioavailability. First, we cover the major cell types found in vivo within the epithelium and microbiota, and discuss how they can be modeled in vitro. We then draw attention to their structural similarities and differences with regard to determinants of drug distribution. Once a drug is solubilized in the luminal fluids, there are two main classes of such determinants: 1) binding processes, and 2) transporters and drug-metabolizing enzymes. Binding lowers the unbound intracellular fraction (fu,cell), which will, in turn, limit the amount of drug available for transport to desired sites. Transporters and drug metabolizing enzymes are ADME proteins impacting intracellular accumulation (Kp). Across cell types, we point out which processes are likely particularly impactful. Together, fu,cell and Kp can be used to describe intracellular bioavailability (Fic), which is a measure of local drug distribution, with consequences for efficacy. Determining these cellular parameters will be beneficial in understanding colonic drug distribution and will advance the field of drug delivery.
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Affiliation(s)
- Rebekkah Hammar
- Department of Pharmacy, Uppsala University, Husargatan 3, 751 23 Uppsala, Sweden
| | - Mikael E Sellin
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Husargatan 3, 751 23 Uppsala, Sweden
| | - Per Artursson
- Department of Pharmacy, Uppsala University, Husargatan 3, 751 23 Uppsala, Sweden.
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Manoj KM, Jacob VD, Kavdia M, Tamagawa H, Jaeken L, Soman V. Questioning rotary functionality in the bacterial flagellar system and proposing a murburn model for motility. J Biomol Struct Dyn 2023; 41:15691-15714. [PMID: 36970840 DOI: 10.1080/07391102.2023.2191146] [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: 11/29/2022] [Accepted: 03/09/2023] [Indexed: 03/29/2023]
Abstract
Bacterial flagellar system (BFS) was the primary example of a purported 'rotary-motor' functionality in a natural assembly. This mandates the translation of a circular motion of components inside into a linear displacement of the cell body outside, which is supposedly orchestrated with the following features of the BFS: (i) A chemical/electrical differential generates proton motive force (pmf, including a trans-membrane potential, TMP), which is electro-mechanically transduced by inward movement of protons via BFS. (ii) Membrane-bound proteins of BFS serve as stators and the slender filament acts as an external propeller, culminating into a hook-rod that pierces the membrane to connect to a 'broader assembly of deterministically movable rotor'. We had disclaimed the purported pmf/TMP-based respiratory/photosynthetic physiology involving Complex V, which was also perceived as a 'rotary machine' earlier. We pointed out that the murburn redox logic was operative therein. We pursue the following similar perspectives in BFS-context: (i) Low probability for the evolutionary attainment of an ordered/synchronized teaming of about two dozen types of proteins (assembled across five-seven distinct phases) towards the singular agendum of rotary motility. (ii) Vital redox activity (not the gambit of pmf/TMP!) powers the molecular and macroscopic activities of cells, including flagella. (iii) Flagellar movement is noted even in ambiances lacking/countering the directionality mandates sought by pmf/TMP. (iv) Structural features of BFS lack component(s) capable of harnessing/achieving pmf/TMP and functional rotation. A viable murburn model for conversion of molecular/biochemical activity into macroscopic/mechanical outcomes is proposed herein for understanding BFS-assisted motility. HIGHLIGHTSThe motor-like functionalism of bacterial flagellar system (BFS) is analyzedProton/Ion-differential based powering of BFS is unviable in bacteriaUncouplers-sponsored effects were misinterpreted, resulting in a detour in BFS researchThese findings mandate new explanation for nano-bio-mechanical movements in BFSA minimalist murburn model for the bacterial flagella-aided movement is proposedCommunicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Kelath Murali Manoj
- Satyamjayatu, The Science & Ethics Foundation, Palakkad District, Kerala, India
| | - Vivian David Jacob
- Satyamjayatu, The Science & Ethics Foundation, Palakkad District, Kerala, India
| | - Mahendra Kavdia
- Department of Biomedical Engineering, Wayne State University, Detroit, Michigan, USA
| | - Hirohisa Tamagawa
- Department of Mechanical Engineering, Gifu University, Gifu City, Japan
| | - Laurent Jaeken
- Department of Industrial Sciences and Technology, Karel de Grote-Hogeschool, Antwerp University Association, Belgium
| | - Vidhu Soman
- Department of Bioscience & Bioengineering, IIT Bombay (& DSS Imagetech Pvt. Ltd), Mumbai, Maharashtra, India
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Exploring the Interspecific Interactions and the Metabolome of the Soil Isolate Hylemonella gracilis. mSystems 2023; 8:e0057422. [PMID: 36537799 PMCID: PMC9948732 DOI: 10.1128/msystems.00574-22] [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] [Indexed: 12/24/2022] Open
Abstract
Microbial community analysis of aquatic environments showed that an important component of its microbial diversity consists of bacteria with cell sizes of ~0.1 μm. Such small bacteria can show genomic reductions and metabolic dependencies with other bacteria. However, so far, no study has investigated if such bacteria exist in terrestrial environments like soil. Here, we isolated soil bacteria that passed through a 0.1-μm filter. The complete genome of one of the isolates was sequenced and the bacterium was identified as Hylemonella gracilis. A set of coculture assays with phylogenetically distant soil bacteria with different cell and genome sizes was performed. The coculture assays revealed that H. gracilis grows better when interacting with other soil bacteria like Paenibacillus sp. AD87 and Serratia plymuthica. Transcriptomics and metabolomics showed that H. gracilis was able to change gene expression, behavior, and biochemistry of the interacting bacteria without direct cell-cell contact. Our study indicates that in soil there are bacteria that can pass through a 0.1-μm filter. These bacteria may have been overlooked in previous research on soil microbial communities. Such small bacteria, exemplified here by H. gracilis, can induce transcriptional and metabolomic changes in other bacteria upon their interactions in soil. In vitro, the studied interspecific interactions allowed utilization of growth substrates that could not be utilized by monocultures, suggesting that biochemical interactions between substantially different sized soil bacteria may contribute to the symbiosis of soil bacterial communities. IMPORTANCE Analysis of aquatic microbial communities revealed that parts of its diversity consist of bacteria with cell sizes of ~0.1 μm. Such bacteria can show genomic reductions and metabolic dependencies with other bacteria. So far, no study investigated if such bacteria exist in terrestrial environments such as soil. Here, we show that such bacteria also exist in soil. The isolated bacteria were identified as Hylemonella gracilis. Coculture assays with phylogenetically different soil bacteria revealed that H. gracilis grows better when cocultured with other soil bacteria. Transcriptomics and metabolomics showed that H. gracilis was able to change gene expression, behavior, and biochemistry of the interacting bacteria without direct contact. Our study revealed that bacteria are present in soil that can pass through 0.1-μm filters. Such bacteria may have been overlooked in previous research on soil microbial communities and may contribute to the symbiosis of soil bacterial communities.
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Herschede SR, Salam R, Gneid H, Busschaert N. Bacterial cytological profiling identifies transmembrane anion transport as the mechanism of action for a urea-based antibiotic. Supramol Chem 2023. [DOI: 10.1080/10610278.2023.2178921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Affiliation(s)
- Sarah R. Herschede
- Department of Chemistry, Tulane University, New Orleans, Louisiana, United States
| | - Rayhanus Salam
- Department of Chemistry, Tulane University, New Orleans, Louisiana, United States
| | - Hassan Gneid
- Department of Chemistry, Tulane University, New Orleans, Louisiana, United States
| | - Nathalie Busschaert
- Department of Chemistry, Tulane University, New Orleans, Louisiana, United States
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36
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Tongthong T, Kaewduangduen W, Phuengmaung P, Chancharoenthana W, Leelahavanichkul A. Lacticaseibacillus rhamnosus dfa1 Attenuate Cecal Ligation-Induced Systemic Inflammation through the Interference in Gut Dysbiosis, Leaky Gut, and Enterocytic Cell Energy. Int J Mol Sci 2023; 24:ijms24043756. [PMID: 36835163 PMCID: PMC9960508 DOI: 10.3390/ijms24043756] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 02/03/2023] [Accepted: 02/06/2023] [Indexed: 02/16/2023] Open
Abstract
Despite an uncommon condition, the clinical management of phlegmon appendicitis (retention of the intra-abdominal appendiceal abscess) is still controversial, and probiotics might be partly helpful. Then, the retained ligated cecal appendage (without gut obstruction) with or without oral Lacticaseibacillus rhamnosus dfa1 (started at 4 days prior to the surgery) was used as a representative model. At 5 days post-surgery, the cecal-ligated mice demonstrated weight loss, soft stool, gut barrier defect (leaky gut using FITC-dextran assay), fecal dysbiosis (increased Proteobacteria with reduced bacterial diversity), bacteremia, elevated serum cytokines, and spleen apoptosis without kidney and liver damage. Interestingly, the probiotics attenuated disease severity as indicated by stool consistency index, FITC-dextran assay, serum cytokines, spleen apoptosis, fecal microbiota analysis (reduced Proteobacteria), and mortality. Additionally, impacts of anti-inflammatory substances from culture media of the probiotics were demonstrated by attenuation of starvation injury in the Caco-2 enterocyte cell line as indicated by transepithelial electrical resistance (TEER), inflammatory markers (supernatant IL-8 with gene expression of TLR4 and NF-κB), cell energy status (extracellular flux analysis), and the reactive oxygen species (malondialdehyde). In conclusion, gut dysbiosis and leaky-gut-induced systemic inflammation might be helpful clinical parameters for patients with phlegmon appendicitis. Additionally, the leaky gut might be attenuated by some beneficial molecules from probiotics.
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Affiliation(s)
- Tongthong Tongthong
- Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
- Center of Excellence in Translational Research in Inflammation and Immunology (CETRII), Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Warerat Kaewduangduen
- Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
- Center of Excellence in Translational Research in Inflammation and Immunology (CETRII), Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Pornpimol Phuengmaung
- Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
- Center of Excellence in Translational Research in Inflammation and Immunology (CETRII), Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Wiwat Chancharoenthana
- Tropical Immunology and Translational Research Unit, Department of Clinical Tropical Medicine, Faculty of Tropical Medicine, Mahidol University, Bangkok 73170, Thailand
| | - Asada Leelahavanichkul
- Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
- Center of Excellence in Translational Research in Inflammation and Immunology (CETRII), Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
- Division of Nephrology, Department of Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
- Correspondence: ; Tel.: +66-2-256-4251
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Xu W, Ceylan Koydemir H. Non-invasive biomedical sensors for early detection and monitoring of bacterial biofilm growth at the point of care. LAB ON A CHIP 2022; 22:4758-4773. [PMID: 36398687 DOI: 10.1039/d2lc00776b] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Bacterial infections have long been a serious global health issue. Biofilm formation complicates matters even more. The biofilm's extracellular polymeric substances (EPSs) matrix protects bacteria from the host's immune responses, yielding strong adhesion and drug resistance as the biofilm matures. Early bacterial biofilm detection and bacterial biofilm growth monitoring are crucial to treating biofilm-associated infections. Current detection methods are highly sensitive but not portable, are time-consuming, and require expensive equipment and complex operating procedures, limiting their use at the point of care. Therefore, there is an urgent need to develop affordable, on-body, and non-invasive biomedical sensors to continuously monitor and detect early biofilm growth at the point of care through personalized telemedicine. Herein, recent advances in developing non-invasive biomedical sensors for early detection and monitoring bacterial biofilm growth are comprehensively reviewed. First, biofilm's life cycle and its impact on the human body, such as biofilm-associated disease and infected medical devices, are introduced together with the challenges of biofilm treatment. Then, the current methods used in clinical and laboratory settings for biofilm detection and their challenges are discussed. Next, the current state of non-invasive sensors for direct and indirect detection of bacterial biofilms are summarized and highlighted with the detection parameters and their design details. Finally, commercially available products, challenges of current devices, and the further trend in biofilm detection sensors are discussed.
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Affiliation(s)
- Weiming Xu
- Department of Biomedical Engineering, Texas A&M University, College Station, 77843, Texas, USA.
- Center for Remote Health Technologies and Systems, Texas A&M Engineering Experiment Station, College Station, 77843, TX, USA
| | - Hatice Ceylan Koydemir
- Department of Biomedical Engineering, Texas A&M University, College Station, 77843, Texas, USA.
- Center for Remote Health Technologies and Systems, Texas A&M Engineering Experiment Station, College Station, 77843, TX, USA
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Page EF, Blake MJ, Foley GA, Calhoun TR. Monitoring membranes: The exploration of biological bilayers with second harmonic generation. CHEMICAL PHYSICS REVIEWS 2022; 3:041307. [PMID: 36536669 PMCID: PMC9756348 DOI: 10.1063/5.0120888] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 11/03/2022] [Indexed: 12/23/2022]
Abstract
Nature's seemingly controlled chaos in heterogeneous two-dimensional cell membranes stands in stark contrast to the precise, often homogeneous, environment in an experimentalist's flask or carefully designed material system. Yet cell membranes can play a direct role, or serve as inspiration, in all fields of biology, chemistry, physics, and engineering. Our understanding of these ubiquitous structures continues to evolve despite over a century of study largely driven by the application of new technologies. Here, we review the insight afforded by second harmonic generation (SHG), a nonlinear optical technique. From potential measurements to adsorption and diffusion on both model and living systems, SHG complements existing techniques while presenting a large exploratory space for new discoveries.
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Affiliation(s)
- Eleanor F. Page
- Department of Chemistry, University of Tennessee, Knoxville, Tennessee 37996, USA
| | - Marea J. Blake
- Department of Chemistry, University of Tennessee, Knoxville, Tennessee 37996, USA
| | - Grant A. Foley
- Department of Chemistry, University of Tennessee, Knoxville, Tennessee 37996, USA
| | - Tessa R. Calhoun
- Department of Chemistry, University of Tennessee, Knoxville, Tennessee 37996, USA
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Garate L, Alonso‐Sáez L, Revilla M, Logares R, Lanzén A. Shared and contrasting associations in the dynamic nano- and picoplankton communities of two close but contrasting sites from the Bay of Biscay. Environ Microbiol 2022; 24:6052-6070. [PMID: 36054533 PMCID: PMC10087561 DOI: 10.1111/1462-2920.16153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 07/30/2022] [Indexed: 01/12/2023]
Abstract
Pico- and nanoplankton are key players in the marine ecosystems due to their implication in the biogeochemical cycles, nutrient recycling and the pelagic food webs. However, the specific dynamics and niches of most bacterial, archaeal and eukaryotic plankton remain unknown, as well as the interactions between them. Better characterization of these is critical for understanding and predicting ecosystem functioning under anthropogenic pressures. We used environmental DNA metabarcoding across a 6-year time series to explore the structure and seasonality of pico- and nanoplankton communities in two sites of the Bay of Biscay, one coastal and one offshore, and construct association networks to reveal potential keystone and connector taxa. Temporal trends in alpha diversity were similar between the two sites, and concurrent communities more similar than within the same site at different times. However, we found differences between the network topologies of the two sites, with both shared and site-specific keystones and connectors. For example, Micromonas, with lower abundance in the offshore site is a keystone here, indicating a stronger effect of associations such as resource competition. This study provides an example of how time series and association network analysis can reveal how similar communities may function differently despite being geographically close.
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Affiliation(s)
- Leire Garate
- AZTI, Marine ResearchBasque Research and Technology Alliance (BRTA)PasaiaSpain
| | - Laura Alonso‐Sáez
- AZTI, Marine ResearchBasque Research and Technology Alliance (BRTA)PasaiaSpain
| | - Marta Revilla
- AZTI, Marine ResearchBasque Research and Technology Alliance (BRTA)PasaiaSpain
| | - Ramiro Logares
- Institute of Marine Sciences (ICM)CSICBarcelonaCataloniaSpain
| | - Anders Lanzén
- AZTI, Marine ResearchBasque Research and Technology Alliance (BRTA)PasaiaSpain
- IKERBASQUEBasque Foundation for ScienceBilbaoBizkaiaSpain
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Experimental Observation of Isolative Efficacy of a Solid Coupling Medium in Extracorporeal Shock Wave Lithotripsy—Implications to Nosocomial Infection Prevention. Pathogens 2022; 11:pathogens11101103. [PMID: 36297160 PMCID: PMC9607363 DOI: 10.3390/pathogens11101103] [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: 09/07/2022] [Revised: 09/25/2022] [Accepted: 09/25/2022] [Indexed: 11/17/2022] Open
Abstract
Introduction: Extracorporeal shock wave lithotripsy (ESWL) is a well-established, popular treatment choice for renal stones. Traditionally, the semi-liquid gel is used as a coupling medium in ESWL. During ESWL, body fluid or blood might transmit between the patients when the probe or gel used in the procedure is contaminated and cause potential nosocomial infections. To solve this problem, we developed a solid coupling medium (isolation coupling pad, referred to as “icPad”) between the patient’s skin and the probe as a shock wave transmission medium to prevent contamination. This study aimed to investigate the isolative efficacy of the icPad in blocking the permeation of microbes. Method: Rhodamine 6G (a fluorescent dye) was used as a tracer to simulate the microorganisms. The penetration of the fluorescent dye on the longitudinal section of the icPad was observed by a microscope after the dye was placed on the body side of the icPad for 40 min. After the shock wave, icPad was extracted with 75% ethanol, and fluorescence intensity was measured with a fluorescence spectrometer. Results: Our results revealed that the body side of icPad is free of fluorescent dye during lithotripsy. Qualitative analysis results confirmed that icPad has an isolative effect on simulating contaminants such as bacteria or viruses. Conclusion: In this in vitro phantom study, a proprietary icPad can be an isolative coupling medium and is speculated to avoid cross-contamination of bacterial or viral infection during ESWL.
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41
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Das S, Datta PP. Effect of a single amino acid substitution G98D in a ribosome-associated essential GTPase, CgtA, on the growth and morphology of Vibrio cholerae. Arch Microbiol 2022; 204:617. [PMID: 36097213 DOI: 10.1007/s00203-022-03233-w] [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: 07/22/2022] [Revised: 08/21/2022] [Accepted: 08/31/2022] [Indexed: 11/02/2022]
Abstract
CgtA, a highly conserved 50S ribosome-associated essential GTPase, acts as a repressor of the stringent stress response under nutrient-rich growth conditions to suppress basal levels of the alarmone ppGpp in V. cholerae. To further explore the in vivo functionality of CgtA, we introduced an amino acid substitution, i.e., Gly98Asp, in a conserved glycine residue in the N-terminal domain. The constructed V. cholerae mutant was designated CgtA(G98D). Comparison of cell sizes of the CgtA(G98D)mutant with its isogenic wild-type (Wt) strain N16961 under different phases of growth by Transmission Electron Microscopy (TEM) and statistical analysis suggests that CgtA may control the cell size of V. cholerae. The cell length is significantly reduced, corresponding to the delayed growth in the mid-logarithmic phase. The differences in the cell length of CgtA(G98D) and Wt are indistinguishable in the late logarithmic phase. During the stationary phase, marked by higher OD600, a sub-population of CgtA(G98D) cells outnumbered the Wt cells lengthwise. CgtA(G98D) cells appeared slenderer than Wt cells with significantly reduced cell width. However, the centerline curvature is preserved in CgtA(G98D) cells. We propose that in addition to its multitude of intracellular roles, CgtA may influence the cell size of V. cholerae.
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Affiliation(s)
- Sagarika Das
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER), Mohanpur, Nadia, Kolkata, 741246, West Bengal, India
| | - Partha Pratim Datta
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER), Mohanpur, Nadia, Kolkata, 741246, West Bengal, India.
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42
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Delgado-Campos A, Cuetos A. Influence of homeostatic mechanisms of bacterial growth and division on structural properties of microcolonies: A computer simulation study. Phys Rev E 2022; 106:034402. [PMID: 36266836 DOI: 10.1103/physreve.106.034402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Accepted: 08/26/2022] [Indexed: 06/16/2023]
Abstract
Bacterial growth and division generally occur by the process known as binary fission, in which the cells grow polarly until they divide into two daughter cells. Although this process is affected by factors that introduce stochastic variability in both growth rate and daughter cell length, the fact is that the size distribution in growing bacteria remains stable over time. This suggests the existence of homeostatic mechanisms that contribute to maintaining a stable size distribution. Those known as sizer and adder stand out among these mechanisms whose relevance is not entirely determined. In this work, computer simulations using an agent-based model are used to study the effect of these homeostatic mechanisms on the geometrical and structural properties of the developing microcolonies, focusing on the early stages of its development. Also, we examine the effect of linear or exponential dependence with the time of cellular growth on these properties. From our study, we deduce that these mechanisms do not have a noticeable impact on the properties studied, which could be due to the importance that stochastic factors play in the cell division and growth process. In addition, we discuss how competition between cell growth and diffusion is a key aspect in explaining the structure and geometry of developing bacterial microcolonies. The results of the study will help to clarify which processes and parameters should be considered relevant when designing simulation models.
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Affiliation(s)
- Andrés Delgado-Campos
- Department of Physical, Chemical and Natural Systems, Pablo de Olavide University, 41013 Seville, Spain
| | - Alejandro Cuetos
- Department of Physical, Chemical and Natural Systems, Pablo de Olavide University, 41013 Seville, Spain
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43
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Zhang Z, He W, Deng Z, Liu Y, Wen H, Wang Y, Ye Z, Kin Kwok RT, Qiu Z, Zhao Z, Tang BZ. A clickable AIEgen for visualization of macrophage-microbe interaction. Biosens Bioelectron 2022; 216:114614. [PMID: 35995026 DOI: 10.1016/j.bios.2022.114614] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 07/27/2022] [Accepted: 07/29/2022] [Indexed: 11/02/2022]
Abstract
Visualization of immunocyte-microbe interaction is of great importance to reveal the physiological role and working mechanism of innate and adaptive immune system. The lack of rapid and stable microbial labeling platform and insufficient understanding of macrophage-microbe interaction may delay precautions that could be made. In this contribution, a clickable AIEgen, CDPP-NCS, containing a cationic pyridinium moiety for targeting bacteria and an isothiocyanate moiety for covalently bonding with amine groups, is successfully developed. With the advantages of excellent photostability and rapid bioconjugation with amine groups on the bacterial envelope, the processes of macrophage-bacterium interactions with subcellular resolution has been successfully captured using this clickable AIE probe. Therefore, the new clickable AIEgen is a powerful tool to study the interaction between cell and bacterium.
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Affiliation(s)
- Zicong Zhang
- School of Science and Engineering, Shenzhen Key Laboratory of Functional Aggregate Materials, The Chinese University of Hong Kong, Shenzhen, Guangdong, 518172, China
| | - Wei He
- Department of Chemistry, Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China; HKUST-Shenzhen Research Institute, South Area Hi-Tech Park, Nanshan, Shenzhen, Guangdong Province, 518057, China
| | - Ziwei Deng
- School of Science and Engineering, Shenzhen Key Laboratory of Functional Aggregate Materials, The Chinese University of Hong Kong, Shenzhen, Guangdong, 518172, China
| | - Yanling Liu
- School of Science and Engineering, Shenzhen Key Laboratory of Functional Aggregate Materials, The Chinese University of Hong Kong, Shenzhen, Guangdong, 518172, China
| | - Haifei Wen
- School of Science and Engineering, Shenzhen Key Laboratory of Functional Aggregate Materials, The Chinese University of Hong Kong, Shenzhen, Guangdong, 518172, China
| | - Yucheng Wang
- School of Science and Engineering, Shenzhen Key Laboratory of Functional Aggregate Materials, The Chinese University of Hong Kong, Shenzhen, Guangdong, 518172, China
| | - Ziyue Ye
- School of Science and Engineering, Shenzhen Key Laboratory of Functional Aggregate Materials, The Chinese University of Hong Kong, Shenzhen, Guangdong, 518172, China
| | - Ryan Tsz Kin Kwok
- Department of Chemistry, Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Zijie Qiu
- School of Science and Engineering, Shenzhen Key Laboratory of Functional Aggregate Materials, The Chinese University of Hong Kong, Shenzhen, Guangdong, 518172, China
| | - Zheng Zhao
- School of Science and Engineering, Shenzhen Key Laboratory of Functional Aggregate Materials, The Chinese University of Hong Kong, Shenzhen, Guangdong, 518172, China; HKUST-Shenzhen Research Institute, South Area Hi-Tech Park, Nanshan, Shenzhen, Guangdong Province, 518057, China.
| | - Ben Zhong Tang
- School of Science and Engineering, Shenzhen Key Laboratory of Functional Aggregate Materials, The Chinese University of Hong Kong, Shenzhen, Guangdong, 518172, China; Department of Chemistry, Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China.
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von Hegner I. Extreme Exoworlds and the Extremophile Paradox. ASTROBIOLOGY 2022; 22:926-936. [PMID: 35787001 DOI: 10.1089/ast.2021.0153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Extremophiles have gained prominence by providing an experimental approach to astrobiology. Extremophiles gain equal value by being part of a framework for high-level characterization of the evolutionary mechanisms that must necessarily restrict or promote their emergence and presence on solar system bodies. Thus, extremophiles exist in extreme environments, and therein lies the paradox: extremophiles can only live in extreme environments but are not able to originate in such environments. Therefore, even though the range of extremophile capabilities in extreme environments is wider than that in mesophiles, the range of their emergence possibilities is still equally restricted. Therefore, even if one locates an extreme exoworld where terrestrial extremophiles could live here-and-now, it can be predicted that no extremophile analogs are present anyway. Furthermore, it is possible for a world to be uninhabited, yet be habitable, and therein arises the extreme environment paradox: an extreme environment can sustain chemical evolution as well as arriving non-native life, yet native life cannot be built up in that very environment. Thus, life may exist on an extraterrestrial extreme world (if imported there), and chemical evolution may be present on that world. However, it can be predicted that there is no native life anyway. This situation can be predicted to function as a chemosignature and eventually as a biosignature. However, the fact that a non-native extremopile in principle can exist in extreme environments may demonstrate that the intermediate step between chemical evolution and extremophiles can still occur in the form of a statistical deviation. In summary, the use of extremophiles as analogs to extraterrestrial life has limitations due to the very conditions evolution operates under, although analysis of these conditions provides conceptual tools for the search for life elsewhere in the Solar System and beyond.
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45
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Ji B, Singh A, Feng J. Water-to-Air Transfer of Nano/Microsized Particulates: Enrichment Effect in Bubble Bursting Jet Drops. NANO LETTERS 2022; 22:5626-5634. [PMID: 35658445 DOI: 10.1021/acs.nanolett.2c01102] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Bubbles dispersed in liquids are widely present in many natural and industrial processes and play a key role in mediating mass transfer during their lifetime from formation to rising to bursting. In particular, nano/microsized particulates and organisms present in the bulk water can be highly enriched in the jet drops ejected during bubble bursting, impacting global climate and public health. However, the detailed mechanism of this enrichment remains obscure with the enrichment factor being difficult to predict. Here, we experimentally investigate the enrichment of nano/microsized particles in bubble bursting jet drops and highlight the underlying hydrodynamic mechanism, combining the effects of bubble scavenge and bursting on the transport of particles. Scaling laws for the enrichment factor are subsequently proposed that describe both our and prior experimental results reasonably well. Our study may provide new insights for water-to-air transfer of bulk particulates such as microbes related to bubble bursting.
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Affiliation(s)
- Bingqiang Ji
- Mechanical Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Amrit Singh
- Mechanical Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Jie Feng
- Mechanical Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Materials Research Laboratory, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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46
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Lee SW, Johnson EL, Chediak JA, Shin H, Wang Y, Phillips KS, Ren D. High-Throughput Biofilm Assay to Investigate Bacterial Interactions with Surface Topographies. ACS APPLIED BIO MATERIALS 2022; 5:3816-3825. [PMID: 35816421 PMCID: PMC9382637 DOI: 10.1021/acsabm.2c00367] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
The specific topography of biomaterials plays an important
role
in their biological interactions with cells and thus the safety of
medical implants. Antifouling materials can be engineered with topographic
features to repel microbes. Meanwhile, undesired topographies of implants
can cause complications such as breast implant-associated anaplastic
large cell lymphoma (BIA-ALCL). While the cause of BIA-ALCL is not
well understood, it is speculated that textured surfaces are prone
to bacterial biofilm formation as a contributing factor. To guide
the design of safer biomaterials and implants, quantitative screening
approaches are needed to assess bacterial adhesion to different topographic
surface features. Here we report the development of a high-throughput
microplate biofilm assay for such screening. The assay was used to
test a library of polydimethylsiloxane (PDMS) textures composed of
varying sizes of recessive features and distances between features
including those in the range of breast implant textures. Outliers
of patterns prone to bacterial adhesion were further studied using
real-time confocal fluorescence microscopy. The results from these
analyses revealed that surface area itself is a poor predictor for
adhesion, while the size and spacing of topographic features play
an important role. This high-throughput biofilm assay can be applied
to studying bacteria–material interactions and rational development
of materials that inhibit bacterial colonization.
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Affiliation(s)
- Sang Won Lee
- Department of Biomedical and Chemical Engineering, Syracuse University, Syracuse, New York 13244, United States.,Office of Medical Products and Tobacco, Center for Devices and Radiological Health, Office of Science and Engineering Laboratories, Division of Biology, Chemistry, and Materials Science, United States Food and Drug Administration, Silver Spring, Maryland 20993, United States
| | - Erick L Johnson
- Mechanical and Industrial Engineering, Montana State University, Bozeman, Montana 59717, United States
| | - J Alex Chediak
- Office of Medical Products and Tobacco, Center for Devices and Radiological Health, Office of Science and Engineering Laboratories, Division of Biology, Chemistry, and Materials Science, United States Food and Drug Administration, Silver Spring, Maryland 20993, United States.,Department of Mathematical Sciences, California Baptist University, Riverside, California 92504, United States
| | - Hainsworth Shin
- Office of Medical Products and Tobacco, Center for Devices and Radiological Health, Office of Science and Engineering Laboratories, Division of Biology, Chemistry, and Materials Science, United States Food and Drug Administration, Silver Spring, Maryland 20993, United States
| | - Yi Wang
- Office of Medical Products and Tobacco, Center for Devices and Radiological Health, Office of Science and Engineering Laboratories, Division of Biology, Chemistry, and Materials Science, United States Food and Drug Administration, Silver Spring, Maryland 20993, United States
| | - K Scott Phillips
- Office of Medical Products and Tobacco, Center for Devices and Radiological Health, Office of Science and Engineering Laboratories, Division of Biology, Chemistry, and Materials Science, United States Food and Drug Administration, Silver Spring, Maryland 20993, United States
| | - Dacheng Ren
- Department of Biomedical and Chemical Engineering, Syracuse University, Syracuse, New York 13244, United States.,Department of Civil and Environmental Engineering, Syracuse University, Syracuse, New York 13244, United States.,Department of Biology, Syracuse University, Syracuse, New York 13244, United States
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Abhijith GR, Ostfeld A. Making waves: Applying systems biology principles in water distribution systems engineering. WATER RESEARCH 2022; 219:118527. [PMID: 35567846 DOI: 10.1016/j.watres.2022.118527] [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: 01/27/2022] [Revised: 04/25/2022] [Accepted: 04/27/2022] [Indexed: 06/15/2023]
Abstract
The complexity of modeling water quality variations in water distribution systems (WDS), studied for decades, stems from multiple constraints and variables involved and the complexity of the system behavior. The conventional macroscale-based WDS water quality models are founded on continuum mechanics. In attempts to provide a broad picture of the multi-species interactions, these models overlook the stochasticity corresponding to the reaction mechanisms within the WDS domain. Furthermore, owing to the black-box type modeling adopted in simulating the multi-species interactions, the existing state-of-the-art models have limitations in representing intermediates and/or by-products formation. Accordingly, they remain ineffective in describing the water chemistry-stoichiometric interactions within the WDS domain. Only a radically new modeling approach could overcome the limitations of the macroscale-based approaches and enables analyzing the stochastic WDS mechanisms by keeping the true nature of the system behavior. Stimulated by the metabolic network modeling principles in systems biology, this article outlines the prospect of developing an innovative 'water'bolic network modeling approach to provide a new outlook to the existing WDS water quality modeling research.
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Affiliation(s)
- Gopinathan R Abhijith
- Civil and Environmental Engineering, Technion - Israel Institute of Technology, Haifa 32000, Israel.
| | - Avi Ostfeld
- Civil and Environmental Engineering, Technion - Israel Institute of Technology, Haifa 32000, Israel
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48
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Nischwitz V, Stelmaszyk L, Piel S, Tiehm A. Cascade Filtration With PCR Detection and Field-Flow-Fractionation Online With ICP-MS for the Characterization of DNA Interaction With Suspended Particulate Matter. Front Chem 2022; 10:919442. [PMID: 35836676 PMCID: PMC9274009 DOI: 10.3389/fchem.2022.919442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 05/18/2022] [Indexed: 12/02/2022] Open
Abstract
The variety of applied antibiotics in animal and human medicine results in the release, development, and spread of relevant numbers of antibiotic resistance genes (ARGs) in the environment. The majority of ARGs are present in intracellular forms (in bacteria). Neglected aspects are extracellular variants of ARGs (eARGs) and their fragments, which have been detected in surface-water samples and sediments. The stability of eARGs is expected to be low; however, binding to particulate matter is likely to improve their stability and also affect their transport and dissemination behavior. Few studies have investigated DNA particle interactions, mostly via indirect characterization of adduct formation in model systems but not in real environmental matrices. Therefore, our study aims at a novel approach for direct characterization of desoxyribonucleic acid (DNA) particle interactions using both cascade filtration and field-flow fractionation. Cascade filtration with quantitative polymerase chain reaction (qPCR) detection indicated retention of ARGs on filters with much larger pore sizes supporting the hypothesis of ARG-particle interactions. However, artifacts from membrane clogging or DNA–membrane interaction cannot be excluded. Consequently, asymmetric flow field-flow fractionation was investigated as an alternative separation technique with the advantage of particle separation in a thin channel, reducing the risk of artifacts. The key method parameters, membrane composition, molecular weight cut off, and carrier composition, were systematically investigated using a calf-thymus DNA-spiked surface-water sample as a model. The results clearly showed a shift in the elution time of clay particles suggesting the presence of DNA–clay adducts. Multi-element detection by inductively coupled plasma mass spectrometry (ICP-MS) enabled monitoring of clay via the Al, Fe, and Si signals and DNA via the P signal. Matching peak profiles for the new fraction in the fractograms of the ARG and DNA-spiked water sample support adduct formation. Further evidence was provided by a novel post-channel filtration approach for the separation of free DNA from DNA–clay adducts.
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Affiliation(s)
- Volker Nischwitz
- Central Institute for Engineering, Electronics and Analytics, Analytics (ZEA-3), Forschungszentrum Juelich, Juelich, Germany
- *Correspondence: Volker Nischwitz,
| | - Lara Stelmaszyk
- Department Water Microbiology, TZW: DVGW Technologiezentrum Wasser, Karlsruhe, Germany
| | - Sandra Piel
- Central Institute for Engineering, Electronics and Analytics, Analytics (ZEA-3), Forschungszentrum Juelich, Juelich, Germany
| | - Andreas Tiehm
- Department Water Microbiology, TZW: DVGW Technologiezentrum Wasser, Karlsruhe, Germany
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Sołtys K, Tarczewska A, Bystranowska D, Sozańska N. Getting Closer to Decrypting the Phase Transitions of Bacterial Biomolecules. Biomolecules 2022; 12:907. [PMID: 35883463 PMCID: PMC9312465 DOI: 10.3390/biom12070907] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 06/24/2022] [Accepted: 06/26/2022] [Indexed: 12/31/2022] Open
Abstract
Liquid-liquid phase separation (LLPS) of biomolecules has emerged as a new paradigm in cell biology, and the process is one proposed mechanism for the formation of membraneless organelles (MLOs). Bacterial cells have only recently drawn strong interest in terms of studies on both liquid-to-liquid and liquid-to-solid phase transitions. It seems that these processes drive the formation of prokaryotic cellular condensates that resemble eukaryotic MLOs. In this review, we present an overview of the key microbial biomolecules that undergo LLPS, as well as the formation and organization of biomacromolecular condensates within the intracellular space. We also discuss the current challenges in investigating bacterial biomacromolecular condensates. Additionally, we highlight a summary of recent knowledge about the participation of bacterial biomolecules in a phase transition and provide some new in silico analyses that can be helpful for further investigations.
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Affiliation(s)
- Katarzyna Sołtys
- Department of Biochemistry, Molecular Biology and Biotechnology, Faculty of Chemistry, Wroclaw University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wroclaw, Poland; (A.T.); (D.B.); (N.S.)
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Volland JM, Gonzalez-Rizzo S, Gros O, Tyml T, Ivanova N, Schulz F, Goudeau D, Elisabeth NH, Nath N, Udwary D, Malmstrom RR, Guidi-Rontani C, Bolte-Kluge S, Davies KM, Jean MR, Mansot JL, Mouncey NJ, Angert ER, Woyke T, Date SV. A centimeter-long bacterium with DNA contained in metabolically active, membrane-bound organelles. Science 2022; 376:1453-1458. [PMID: 35737788 DOI: 10.1126/science.abb3634] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Cells of most bacterial species are around 2 micrometers in length, with some of the largest specimens reaching 750 micrometers. Using fluorescence, x-ray, and electron microscopy in conjunction with genome sequencing, we characterized Candidatus (Ca.) Thiomargarita magnifica, a bacterium that has an average cell length greater than 9000 micrometers and is visible to the naked eye. These cells grow orders of magnitude over theoretical limits for bacterial cell size, display unprecedented polyploidy of more than half a million copies of a very large genome, and undergo a dimorphic life cycle with asymmetric segregation of chromosomes into daughter cells. These features, along with compartmentalization of genomic material and ribosomes in translationally active organelles bound by bioenergetic membranes, indicate gain of complexity in the Thiomargarita lineage and challenge traditional concepts of bacterial cells.
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Affiliation(s)
- Jean-Marie Volland
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,Laboratory for Research in Complex Systems, Menlo Park, CA, USA
| | - Silvina Gonzalez-Rizzo
- Institut de Systématique, Evolution, Biodiversité, Université des Antilles, Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Campus de Fouillole, Pointe-à-Pitre, France
| | - Olivier Gros
- Institut de Systématique, Evolution, Biodiversité, Université des Antilles, Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Campus de Fouillole, Pointe-à-Pitre, France.,Centre Commun de Caractérisation des Matériaux des Antilles et de la Guyane, Université des Antilles, UFR des Sciences Exactes et Naturelles, Pointe-à-Pitre, Guadeloupe, France
| | - Tomáš Tyml
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,Laboratory for Research in Complex Systems, Menlo Park, CA, USA
| | - Natalia Ivanova
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Frederik Schulz
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Danielle Goudeau
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Nathalie H Elisabeth
- Department of Energy Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Nandita Nath
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Daniel Udwary
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Rex R Malmstrom
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Chantal Guidi-Rontani
- Institut de Systématique, Evolution, Biodiversité CNRS UMR 7205, Museum National d'Histoire Naturelle, Paris, France
| | - Susanne Bolte-Kluge
- Sorbonne Universités, UPMC Univ. Paris 06, CNRS FRE3631, Institut de Biologie Paris Seine, Paris, France
| | - Karen M Davies
- Department of Energy Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,Department of Molecular and Cell Biology, University of California, Berkeley, USA
| | - Maïtena R Jean
- Institut de Systématique, Evolution, Biodiversité, Université des Antilles, Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Campus de Fouillole, Pointe-à-Pitre, France
| | - Jean-Louis Mansot
- Centre Commun de Caractérisation des Matériaux des Antilles et de la Guyane, Université des Antilles, UFR des Sciences Exactes et Naturelles, Pointe-à-Pitre, Guadeloupe, France
| | - Nigel J Mouncey
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Esther R Angert
- Cornell University, College of Agriculture and Life Sciences, Department of Microbiology, Ithaca, NY, USA
| | - Tanja Woyke
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,Laboratory for Research in Complex Systems, Menlo Park, CA, USA.,University of California Merced, School of Natural Sciences, Merced, CA, USA
| | - Shailesh V Date
- Laboratory for Research in Complex Systems, Menlo Park, CA, USA.,University of California San Francisco, San Francisco, CA, USA.,San Francisco State University, San Francisco, CA, USA
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