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Forni D, Pozzoli U, Mozzi A, Cagliani R, Sironi M. Depletion of CpG dinucleotides in bacterial genomes may represent an adaptation to high temperatures. NAR Genom Bioinform 2024; 6:lqae088. [PMID: 39071851 PMCID: PMC11282364 DOI: 10.1093/nargab/lqae088] [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: 03/18/2024] [Revised: 06/17/2024] [Accepted: 07/18/2024] [Indexed: 07/30/2024] Open
Abstract
Dinucleotide biases have been widely investigated in the genomes of eukaryotes and viruses, but not in bacteria. We assembled a dataset of bacterial genomes (>15 000), which are representative of the genetic diversity in the kingdom Eubacteria, and we analyzed dinucleotide biases in relation to different traits. We found that TpA dinucleotides are the most depleted and that CpG dinucleotides show the widest dispersion. The abundances of both dinucleotides vary with genomic G + C content and show a very strong phylogenetic signal. After accounting for G + C content and phylogenetic inertia, we analyzed different bacterial lifestyle traits. We found that temperature preferences associate with the abundance of CpG dinucleotides, with thermophiles/hyperthemophiles being particularly depleted. Conversely, the TpA dinucleotide displays a bias that only depends on genomic G + C composition. Using predictions of intrinsic cyclizability we also show that CpG depletion may associate with higher DNA bendability in both thermophiles/hyperthermophiles and mesophiles, and that the former are predicted to have significantly more flexible genomes than the latter. We suggest that higher bendability is advantageous at high temperatures because it facilitates DNA positive supercoiling and that, through modulation of DNA mechanical properties, local or global CpG depletion controls genome organization, most likely not only in bacteria.
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Affiliation(s)
- Diego Forni
- Scientific Institute IRCCS E. MEDEA, Bioinformatics, 23842 Bosisio Parini, Italy
| | - Uberto Pozzoli
- Scientific Institute IRCCS E. MEDEA, Bioinformatics, 23842 Bosisio Parini, Italy
| | - Alessandra Mozzi
- Scientific Institute IRCCS E. MEDEA, Bioinformatics, 23842 Bosisio Parini, Italy
| | - Rachele Cagliani
- Scientific Institute IRCCS E. MEDEA, Bioinformatics, 23842 Bosisio Parini, Italy
| | - Manuela Sironi
- Scientific Institute IRCCS E. MEDEA, Bioinformatics, 23842 Bosisio Parini, Italy
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2
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Kalapos MP, de Bari L. The evolutionary arch of bioenergetics from prebiotic mechanisms to the emergence of a cellular respiratory chain. Biosystems 2024; 244:105288. [PMID: 39128646 DOI: 10.1016/j.biosystems.2024.105288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2024] [Revised: 08/07/2024] [Accepted: 08/07/2024] [Indexed: 08/13/2024]
Abstract
This article proposes an evolutionary trajectory for the development of biological energy producing systems. Six main stages of energy producing system evolution are described, from early evolutionary pyrite-pulled mechanism through the Last Universal Common Ancestor (LUCA) to contemporary systems. We define the Last Pure Chemical Entity (LPCE) as the last completely non-enzymatic entity. LPCE could have had some life-like properties, but lacked genetic information carriers, thus showed greater instability and environmental dependence than LUCA. A double bubble model is proposed for compartmentalization and cellularization as a prerequisite to both highly efficient protein synthesis and transmembrane ion-gradient. The article finds that although LUCA predominantly functioned anaerobically, it was a non-exclusive anaerobe, and sulfur dominated metabolism preceded phosphate dominated one.
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Affiliation(s)
| | - Lidia de Bari
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, Bari, Italy
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3
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Shabestary K, Klemm C, Carling B, Marshall J, Savigny J, Storch M, Ledesma-Amaro R. Phenotypic heterogeneity follows a growth-viability tradeoff in response to amino acid identity. Nat Commun 2024; 15:6515. [PMID: 39095345 PMCID: PMC11297284 DOI: 10.1038/s41467-024-50602-8] [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: 02/02/2024] [Accepted: 07/16/2024] [Indexed: 08/04/2024] Open
Abstract
In their natural environments, microorganisms mainly operate at suboptimal growth conditions with fluctuations in nutrient abundance. The resulting cellular adaptation is subject to conflicting tasks: growth or survival maximisation. Here, we study this adaptation by systematically measuring the impact of a nitrogen downshift to 24 nitrogen sources on cellular metabolism at the single-cell level. Saccharomyces lineages grown in rich media and exposed to a nitrogen downshift gradually differentiate to form two subpopulations of different cell sizes where one favours growth while the other favours viability with an extended chronological lifespan. This differentiation is asymmetrical with daughter cells representing the new differentiated state with increased viability. We characterise the metabolic response of the subpopulations using RNA sequencing, metabolic biosensors and a transcription factor-tagged GFP library coupled to high-throughput microscopy, imaging more than 800,000 cells. We find that the subpopulation with increased viability is associated with a dormant quiescent state displaying differences in MAPK signalling. Depending on the identity of the nitrogen source present, differentiation into the quiescent state can be actively maintained, attenuated, or aborted. These results establish amino acids as important signalling molecules for the formation of genetically identical subpopulations, involved in chronological lifespan and growth rate determination.
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Affiliation(s)
- Kiyan Shabestary
- Department of Bioengineering and Imperial College Centre for Synthetic Biology, Imperial College London, London, SW7 2AZ, UK.
| | - Cinzia Klemm
- Department of Bioengineering and Imperial College Centre for Synthetic Biology, Imperial College London, London, SW7 2AZ, UK
| | - Benedict Carling
- Department of Bioengineering and Imperial College Centre for Synthetic Biology, Imperial College London, London, SW7 2AZ, UK
- London Biofoundry, Imperial College Translation & Innovation Hub, London, UK
| | - James Marshall
- Department of Bioengineering and Imperial College Centre for Synthetic Biology, Imperial College London, London, SW7 2AZ, UK
- London Biofoundry, Imperial College Translation & Innovation Hub, London, UK
| | - Juline Savigny
- Department of Bioengineering and Imperial College Centre for Synthetic Biology, Imperial College London, London, SW7 2AZ, UK
| | - Marko Storch
- London Biofoundry, Imperial College Translation & Innovation Hub, London, UK
- Department of Infectious Disease, Imperial College London, London, SW7 2AZ, UK
| | - Rodrigo Ledesma-Amaro
- Department of Bioengineering and Imperial College Centre for Synthetic Biology, Imperial College London, London, SW7 2AZ, UK.
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4
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Preminger N, Schuldiner M. Beyond fission and fusion-Diving into the mysteries of mitochondrial shape. PLoS Biol 2024; 22:e3002671. [PMID: 38949997 PMCID: PMC11216622 DOI: 10.1371/journal.pbio.3002671] [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] [Indexed: 07/03/2024] Open
Abstract
Mitochondrial shape and network formation have been primarily associated with the well-established processes of fission and fusion. However, recent research has unveiled an intricate and multifaceted landscape of mitochondrial morphology that extends far beyond the conventional fission-fusion paradigm. These less-explored dimensions harbor numerous unresolved mysteries. This review navigates through diverse processes influencing mitochondrial shape and network formation, highlighting the intriguing complexities and gaps in our understanding of mitochondrial architecture. The exploration encompasses various scales, from biophysical principles governing membrane dynamics to molecular machineries shaping mitochondria, presenting a roadmap for future research in this evolving field.
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Affiliation(s)
- Noga Preminger
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Maya Schuldiner
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
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5
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Caliskan-Aydogan O, Zaborney Kline C, Alocilja EC. Cell morphology as biomarker of carbapenem exposure. J Antibiot (Tokyo) 2024:10.1038/s41429-024-00749-9. [PMID: 38866921 DOI: 10.1038/s41429-024-00749-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 05/20/2024] [Accepted: 05/23/2024] [Indexed: 06/14/2024]
Abstract
Characterizing the physiological response of bacterial cells to antibiotics is crucial for designing diagnostic techniques, treatment choices, and drug development. While bacterial cells at sublethal doses of antibiotics are commonly characterized, the impact of exposure to high concentrations of antibiotics on bacteria after long-term serial exposure and their effect on withdrawal need attention for further characterization. This study investigated the effect of increasing imipenem concentrations on carbapenem-susceptible (S) and carbapenem-resistant (R) E. coli on their growth adaptation and cell surface structure. We exposed the bacterial population to increasing imipenem concentrations through 30 exposure cycles. Cell morphology was observed using a 3D laser scanning confocal microscope (LSCM) and transmission electron microscope (TEM). Results showed that the exposure resulted in significant morphological changes in E. coli (S) cells, while minor changes were seen in E. coli (R) cells. The rod-shaped E. coli (S) gradually transformed into round shapes. Further, the exposed E. coli (S) cells' surface area-to-volume ratio (SA/V) was also significantly different from the control, which is non-exposed E. coli (S). Then, the exposed E. coli (S) cells were re-grown in antibiotic-free environment for 100 growth cycles to determine if the changes in cells were reversible. The results showed that their cell morphology remained round, showing that the cell morphology was not reversible. The morphological response of these cells to imipenem can assist in understanding the resistance mechanism in the context of diagnostics and antibacterial therapies.
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Affiliation(s)
- Oznur Caliskan-Aydogan
- Department of Biosystems and Agricultural Engineering, Michigan State University, East Lansing, MI, 48824, USA
- Global Alliance for Rapid Diagnostics (GARD), Michigan State University, East Lansing, MI, 48824, USA
| | - Chloe Zaborney Kline
- Department of Biosystems and Agricultural Engineering, Michigan State University, East Lansing, MI, 48824, USA
| | - Evangelyn C Alocilja
- Department of Biosystems and Agricultural Engineering, Michigan State University, East Lansing, MI, 48824, USA.
- Global Alliance for Rapid Diagnostics (GARD), Michigan State University, East Lansing, MI, 48824, USA.
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6
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Sakai M, Shimosaka T, Katsumata K, Yohda M, Narumi I. Developing a new host-vector system for Deinococcus grandis. Front Microbiol 2024; 15:1387296. [PMID: 38863757 PMCID: PMC11165121 DOI: 10.3389/fmicb.2024.1387296] [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: 02/17/2024] [Accepted: 04/26/2024] [Indexed: 06/13/2024] Open
Abstract
Deinococcus spp. are known for their radiation resistance, toxic compound removal, and production of valuable substances. Therefore, developing gene expression systems for Deinococcus spp. is crucial in advancing genetic engineering applications. To date, plasmid vectors that express foreign genes in D. radiodurans and D. geothermalis have been limited to plasmid pI3 and its derivatives. In contrast, plasmid vectors that express foreign genes in D. grandis include plasmid pZT23 and its derivatives. In this study, we developed a new system for the stable introduction and retention of expression plasmids for D. grandis. Two cryptic plasmids were removed from the wild-type strain to generate the TY3 strain. We then constructed a shuttle vector plasmid, pGRC5, containing the replication initiation region of the smallest cryptic plasmid, pDEGR-3, replication initiation region of the E. coli vector, pACYC184, and an antibiotic resistance gene. We introduced pGRC5, pZT23-derived plasmid pZT29H, and pI3-derived plasmid pRADN8 into strain TY3, and found their coexistence in D. grandis cells. The quantitative PCR assay results found that pGRC5, pZT29H, and pRADN8 had relative copy numbers of 11, 26, and 5 per genome, respectively. Furthermore, we developed a new plasmid in which the luciferase gene was controlled by the promoter region, which contained radiation-desiccation response operator sequences for D. grandis DdrO, a stress response regulon repressor in D. grandis, hence inducing gene expression via ultraviolet-C light irradiation. These plasmids are expected to facilitate the removal and production of toxic and valuable substances, in D. grandis, respectively, particularly of those involving multiple genes.
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Affiliation(s)
- Miyabi Sakai
- Department of Biotechnology and Life Science, Faculty of Engineering, Tokyo University of Agriculture and Technology, Koganei, Tokyo, Japan
| | - Taichi Shimosaka
- Department of Life Sciences, Faculty of Life Sciences, Toyo University, Asaka, Japan
| | | | - Masafumi Yohda
- Department of Biotechnology and Life Science, Faculty of Engineering, Tokyo University of Agriculture and Technology, Koganei, Tokyo, Japan
| | - Issay Narumi
- Department of Life Sciences, Faculty of Life Sciences, Toyo University, Asaka, Japan
- Graduate School of Life Sciences, Toyo University, Asaka, Japan
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7
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Lu Z, Cai Q, Lai S, Chen N, Huang L, Liu Y, Lei L, Gan S, Zhang L, Paerl HW, Wang F. Coupling of cylindrospermopsin and pho-harboring Verrucomicrobia supports the formation of Raphidiopsis blooms in low-phosphorus waters. WATER RESEARCH 2024; 250:121010. [PMID: 38142507 DOI: 10.1016/j.watres.2023.121010] [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: 08/18/2023] [Revised: 10/26/2023] [Accepted: 12/10/2023] [Indexed: 12/26/2023]
Abstract
Cylindrospermopsin (CYN) can induce phytoplankton community to secrete alkaline phosphatase (ALP), which is one of the important strategies for the bloom-forming cyanobacterium Raphidiopsis to thrive in extremely low-phosphorus (P) waters. However, how bacterioplankton community, another major contributor to ALPs in waters, couples to Raphidiopsis through CYN, and the role of this coupling in supporting the dominance of Raphidiopsis in nature remain largely unknown. Here, we conducted microcosm experiments to address this knowledge gap, using a combination of differential filtration-based and metagenomics-based methods to identify the sources of ALPs. We found that, compared with algal-derived ALPs, bacteria-derived ALPs exhibited a more pronounced and sensitive response to CYN. This response to CYN was enhanced under low-P conditions. Interestingly, we found that Verrucomicrobia made the largest contribution to the total abundance of pho genes, which encode ALPs. Having high gene abundance of the CYN-sensing PI3K-AKT signaling pathway, Verrucomicrobia's proportion increased with higher concentrations of CYN under low-P conditions, thereby explaining the observed increase in pho gene abundance. Compared with other cyanobacterial genera, Raphidiopsis had a higher abundance of the pst gene. This suggests that Raphidiopsis exhibited a greater capacity to uptake the inorganic P generated by ALPs secreted by other organisms. Overall, our results reveal the mechanism of CYN-induced ALP secretion and its impact on planktonic P-cycling, and provide valuable insights into the role of CYN in supporting the formation of Raphidiopsis blooms.
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Affiliation(s)
- Zhe Lu
- Xiaoliang Research Station of Tropical Coastal Ecosystems, Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, the CAS Engineering Laboratory for Ecological Restoration of Island and Coastal Ecosystems, and Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, PR China; South China National Botanical Garden, Guangzhou 510650, PR China.
| | - Qijia Cai
- State Environmental Protection Key Laboratory of Environmental Pollution Health Risk Assessment, South China Institute of Environmental Sciences, Guangzhou, 510655, PR China
| | - Shuyan Lai
- Department of Ecology and Institute of Hydrobiology, Jinan University, Guangzhou, 510650, PR China
| | - Nan Chen
- Department of Ecology and Institute of Hydrobiology, Jinan University, Guangzhou, 510650, PR China
| | - Lincheng Huang
- College of Marine Sciences, South China Agricultural University, Guangzhou, 510650, PR China
| | - Yongxin Liu
- College of Marine Sciences, South China Agricultural University, Guangzhou, 510650, PR China
| | - Lamei Lei
- Department of Ecology and Institute of Hydrobiology, Jinan University, Guangzhou, 510650, PR China.
| | - Shuchai Gan
- Xiaoliang Research Station of Tropical Coastal Ecosystems, Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, the CAS Engineering Laboratory for Ecological Restoration of Island and Coastal Ecosystems, and Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, PR China; South China National Botanical Garden, Guangzhou 510650, PR China
| | - Lulu Zhang
- Xiaoliang Research Station of Tropical Coastal Ecosystems, Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, the CAS Engineering Laboratory for Ecological Restoration of Island and Coastal Ecosystems, and Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, PR China; South China National Botanical Garden, Guangzhou 510650, PR China
| | - Hans W Paerl
- Institute of Marine Sciences, The University of North Carolina at Chapel Hill, Morehead City, USA
| | - Faming Wang
- Xiaoliang Research Station of Tropical Coastal Ecosystems, Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, the CAS Engineering Laboratory for Ecological Restoration of Island and Coastal Ecosystems, and Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, PR China; South China National Botanical Garden, Guangzhou 510650, PR China.
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8
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Wang Y, Wu Z, Wang Z, Du H, Xiao S, Lu L, Wang Z. Analyses of the Antibiofilm Activity of o-Phenanthroline Monohydrate against Enterococcus faecalis and Staphylococcus aureus and the Mechanisms Underlying These Effects. ACS Infect Dis 2024; 10:638-649. [PMID: 38258383 DOI: 10.1021/acsinfecdis.3c00516] [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: 01/24/2024]
Abstract
Enterococcus faecalis and Staphylococcus aureus exhibit robust biofilm formation capabilities, the formation of which is closely linked to pathogenicity and drug resistance, thereby resulting in host infection and treatment failure. o-Phenanthroline monohydrate (o-Phen) and its derivatives demonstrate a wide range of antibacterial and antifungal activities. In this study, we aimed to explore the antibiofilm activity of o-Phen to E. faecalis and S. aureus and provide insights into the molecular mechanisms for combating biofilm resistance. We demonstrated that o-Phen possesses significant antibacterial and antibiofilm properties against E. faecalis and S. aureus, inducing alterations in bacterial morphology, compromising cell membrane integrity, and exhibiting synergistic effects with β-lactam antibiotics at sub-MIC concentrations. The adhesion ability and automatic condensation capacity of, and synthesis of, extracellular polymers by E. faecalis cells were reduced by o-Phen, resulting in the inhibition of biofilm formation. Importantly, transcriptome analysis revealed 354 upregulated and 456 downregulated genes in o-Phen-treated E. faecalis. Differentially expressed genes were enriched in 11 metabolism-related pathways, including amino acid metabolism, pyrimidine metabolism, and glycolysis/gluconeogenesis. Moreover, the oppA, CeuA, and ZnuB genes involved in the ABC transport system, and the PBP1A penicillin-binding protein-coding genes sarA and mrcA were significantly downregulated. The multidrug efflux pump system and membrane permeability genes mdtG and hlyD, and bacterial adhesion-related genes, including adcA and fss2 were also downregulated, while mraZ and ASP23 were upregulated. Thus, o-Phen is anticipated to be an effective alternative drug for the treatment of E. faecalis and S. aureus biofilm-associated infections.
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Affiliation(s)
- Yu Wang
- Beijing Key Laboratory of Traditional Chinese Veterinary Medicine, Animal Science and Technology College, Beijing University of Agriculture, Beijing 102206, China
| | - Zhouhui Wu
- Beijing Key Laboratory of Traditional Chinese Veterinary Medicine, Animal Science and Technology College, Beijing University of Agriculture, Beijing 102206, China
| | - Zhiwen Wang
- Beijing Key Laboratory of Traditional Chinese Veterinary Medicine, Animal Science and Technology College, Beijing University of Agriculture, Beijing 102206, China
| | - Heng Du
- Beijing Key Laboratory of Traditional Chinese Veterinary Medicine, Animal Science and Technology College, Beijing University of Agriculture, Beijing 102206, China
| | - Shuang Xiao
- Beijing Key Laboratory of Traditional Chinese Veterinary Medicine, Animal Science and Technology College, Beijing University of Agriculture, Beijing 102206, China
| | - Lin Lu
- Beijing Key Laboratory of Traditional Chinese Veterinary Medicine, Animal Science and Technology College, Beijing University of Agriculture, Beijing 102206, China
| | - Zhen Wang
- Beijing Key Laboratory of Traditional Chinese Veterinary Medicine, Animal Science and Technology College, Beijing University of Agriculture, Beijing 102206, China
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9
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Flamholz AI, Goyal A, Fischer WW, Newman DK, Phillips R. The proteome is a terminal electron acceptor. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.31.578293. [PMID: 38352589 PMCID: PMC10862836 DOI: 10.1101/2024.01.31.578293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/25/2024]
Abstract
Microbial metabolism is impressively flexible, enabling growth even when available nutrients differ greatly from biomass in redox state. E. coli, for example, rearranges its physiology to grow on reduced and oxidized carbon sources through several forms of fermentation and respiration. To understand the limits on and evolutionary consequences of metabolic flexibility, we developed a mathematical model coupling redox chemistry with principles of cellular resource allocation. Our integrated model clarifies key phenomena, including demonstrating that autotrophs grow slower than heterotrophs because of constraints imposed by intracellular production of reduced carbon. Our model further indicates that growth is improved by adapting the redox state of biomass to nutrients, revealing an unexpected mode of evolution where proteins accumulate mutations benefiting organismal redox balance.
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Affiliation(s)
- Avi I. Flamholz
- Division of Biology and Biological Engineering, California Institute of Technology; Pasadena, CA 91125
| | - Akshit Goyal
- Physics of Living Systems, Department of Physics, Massachusetts Institute of Technology; Cambridge, MA 02139
- International Centre for Theoretical Sciences, Tata Institute of Fundamental Research; Bengaluru 560089
| | - Woodward W. Fischer
- Division of Geological & Planetary Sciences, California Institute of Technology; Pasadena, CA 91125
| | - Dianne K. Newman
- Division of Biology and Biological Engineering, California Institute of Technology; Pasadena, CA 91125
- Division of Geological & Planetary Sciences, California Institute of Technology; Pasadena, CA 91125
| | - Rob Phillips
- Division of Biology and Biological Engineering, California Institute of Technology; Pasadena, CA 91125
- Department of Physics, California Institute of Technology; Pasadena, CA 91125, USA
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10
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Govers SK, Campos M, Tyagi B, Laloux G, Jacobs-Wagner C. Apparent simplicity and emergent robustness in the control of the Escherichia coli cell cycle. Cell Syst 2024; 15:19-36.e5. [PMID: 38157847 DOI: 10.1016/j.cels.2023.12.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 06/15/2023] [Accepted: 12/01/2023] [Indexed: 01/03/2024]
Abstract
To examine how bacteria achieve robust cell proliferation across diverse conditions, we developed a method that quantifies 77 cell morphological, cell cycle, and growth phenotypes of a fluorescently labeled Escherichia coli strain and >800 gene deletion derivatives under multiple nutrient conditions. This approach revealed extensive phenotypic plasticity and deviating mutant phenotypes were often nutrient dependent. From this broad phenotypic landscape emerged simple and robust unifying rules (laws) that connect DNA replication initiation, nucleoid segregation, FtsZ ring formation, and cell constriction to specific aspects of cell size (volume, length, or added length) at the population level. Furthermore, completion of cell division followed the initiation of cell constriction after a constant time delay across strains and nutrient conditions, identifying cell constriction as a key control point for cell size determination. Our work provides a population-level description of the governing principles by which E. coli integrates cell cycle processes and growth rate with cell size to achieve its robust proliferative capability. A record of this paper's transparent peer review process is included in the supplemental information.
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Affiliation(s)
- Sander K Govers
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA; de Duve Institute, UCLouvain, Brussels, Belgium; Department of Biology, KU Leuven, Leuven, Belgium
| | - Manuel Campos
- Centre de Biologie Intégrative de Toulouse, Laboratoire de Microbiologie et Génétique Moléculaires, Université de Toulouse, Toulouse, France
| | - Bhavyaa Tyagi
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA; Department of Biology, Stanford University, Stanford, CA 94305, USA
| | | | - Christine Jacobs-Wagner
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA; Department of Biology, Stanford University, Stanford, CA 94305, USA; Sarafan Chemistry, Engineering Medicine for Human Health Institute, Stanford University, Stanford, CA 94305, USA; Department of Microbiology and Immunology, Stanford School of Medicine, Stanford, CA 94305, USA.
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11
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Choi HW, Park SE, Kim EJ, Seo SH, Woong Whon T, Son HS. Effects of ingredient size on microbial communities and metabolites of radish kimchi. Food Chem X 2023; 20:100950. [PMID: 38144756 PMCID: PMC10739756 DOI: 10.1016/j.fochx.2023.100950] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 10/16/2023] [Accepted: 10/17/2023] [Indexed: 12/26/2023] Open
Abstract
In this study, changes in physicochemical characteristics, microbial communities, and metabolites were investigated to identify the fermentation characteristics of radish kimchi according to the size of radish cubes used. The small-sized radish kimchi group showed the highest hardness value and glucose content in the early stages of fermentation. The relative abundance of major lactic acid bacteria, including Leuconostoc, Weissella, and Lactobacillus, was the highest in the small-sized radish kimchi group on day 5 of fermentation, which resulted in rapid production of lactic acid, thereby causing a decrease in pH and an increase in titratable acidity. The size of the radish in kimchi plays a pivotal role in determining various factors, most notably during the first 5 days of fermentation, leading to marked metabolic changes. A total of 17 metabolites, including glucose, sucrose, lactic acid, malic acid, citric acid, and GABA, exhibited significant differences in the small-size radish kimchi group. Interestingly, the sucrose content was higher in the large-sized radish group at the beginning of fermentation. This study revealed that ingredient size can selectively affect the growth of specific microorganisms in an environment where several microorganisms coexist, which could change the quality of radish kimchi.
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Affiliation(s)
- Hyun-Woong Choi
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul 02841, Republic of Korea
| | - Seong-Eun Park
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul 02841, Republic of Korea
| | - Eun-Ju Kim
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul 02841, Republic of Korea
| | | | - Tae Woong Whon
- Kimchi Functionality Research Group, World Institute of Kimchi, Gwangju 61755, Republic of Korea
| | - Hong-Seok Son
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul 02841, Republic of Korea
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12
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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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13
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Matsumoto N, Matsutani M, Tanimoto Y, Nakanishi R, Tanaka S, Kanesaki Y, Theeragool G, Kataoka N, Yakushi T, Matsushita K. Implication of amino acid metabolism and cell surface integrity for the thermotolerance mechanism in the thermally adapted acetic acid bacterium Acetobacter pasteurianus TH-3. J Bacteriol 2023; 205:e0010123. [PMID: 37930061 PMCID: PMC10662122 DOI: 10.1128/jb.00101-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 10/19/2023] [Indexed: 11/07/2023] Open
Abstract
IMPORTANCE Acetobacter pasteurianus, an industrial vinegar-producing strain, is suffered by fermentation stress such as fermentation heat and/or high concentrations of acetic acid. By an experimental evolution approach, we have obtained a stress-tolerant strain, exhibiting significantly increased growth and acetic acid fermentation ability at higher temperatures. In this study, we report that only the three gene mutations of ones accumulated during the adaptation process, ansP, dctD, and glnD, were sufficient to reproduce the increased thermotolerance of A. pasteurianus. These mutations resulted in cell envelope modification, including increased phospholipid and lipopolysaccharide synthesis, increased respiratory activity, and cell size reduction. The phenotypic changes may cooperatively work to make the adapted cell thermotolerant by enhancing cell surface integrity, nutrient or oxygen availability, and energy generation.
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Affiliation(s)
- Nami Matsumoto
- Department of Biological Chemistry, Faculty of Agriculture, Yamaguchi University, Yamaguchi, Japan
- Graduate School of Science and Technology for Innovation, Yamaguchi University, Yamaguchi, Japan
| | - Minenosuke Matsutani
- Department of Biological Chemistry, Faculty of Agriculture, Yamaguchi University, Yamaguchi, Japan
- Graduate School of Science and Technology for Innovation, Yamaguchi University, Yamaguchi, Japan
- NODAI Genome Research Center, Tokyo University of Agriculture, Tokyo, Japan
| | - Yoko Tanimoto
- Department of Biological Chemistry, Faculty of Agriculture, Yamaguchi University, Yamaguchi, Japan
| | - Rina Nakanishi
- Graduate School of Science and Technology for Innovation, Yamaguchi University, Yamaguchi, Japan
| | - Shuhei Tanaka
- Department of Biological Chemistry, Faculty of Agriculture, Yamaguchi University, Yamaguchi, Japan
- Graduate School of Science and Technology for Innovation, Yamaguchi University, Yamaguchi, Japan
| | - Yu Kanesaki
- NODAI Genome Research Center, Tokyo University of Agriculture, Tokyo, Japan
- Research Institute of Green Science and Technology, Shizuoka University, , Shizuoka, Japan
| | - Gunjana Theeragool
- Department of Microbiology, Faculty of Science, Kasetsart University, Bangkok, Thailand
| | - Naoya Kataoka
- Department of Biological Chemistry, Faculty of Agriculture, Yamaguchi University, Yamaguchi, Japan
- Graduate School of Science and Technology for Innovation, Yamaguchi University, Yamaguchi, Japan
- Research Center for Thermotolerant Microbial Resources, Yamaguchi University, Yamaguchi, Japan
| | - Toshiharu Yakushi
- Department of Biological Chemistry, Faculty of Agriculture, Yamaguchi University, Yamaguchi, Japan
- Graduate School of Science and Technology for Innovation, Yamaguchi University, Yamaguchi, Japan
- Research Center for Thermotolerant Microbial Resources, Yamaguchi University, Yamaguchi, Japan
| | - Kazunobu Matsushita
- Department of Biological Chemistry, Faculty of Agriculture, Yamaguchi University, Yamaguchi, Japan
- Graduate School of Science and Technology for Innovation, Yamaguchi University, Yamaguchi, Japan
- Research Center for Thermotolerant Microbial Resources, Yamaguchi University, Yamaguchi, Japan
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14
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Matamouros S, Gensch T, Cerff M, Sachs CC, Abdollahzadeh I, Hendriks J, Horst L, Tenhaef N, Tenhaef J, Noack S, Graf M, Takors R, Nöh K, Bott M. Growth-rate dependency of ribosome abundance and translation elongation rate in Corynebacterium glutamicum differs from that in Escherichia coli. Nat Commun 2023; 14:5611. [PMID: 37699882 PMCID: PMC10497606 DOI: 10.1038/s41467-023-41176-y] [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: 04/09/2021] [Accepted: 08/24/2023] [Indexed: 09/14/2023] Open
Abstract
Bacterial growth rate (µ) depends on the protein synthesis capacity of the cell and thus on the number of active ribosomes and their translation elongation rate. The relationship between these fundamental growth parameters have only been described for few bacterial species, in particular Escherichia coli. Here, we analyse the growth-rate dependency of ribosome abundance and translation elongation rate for Corynebacterium glutamicum, a gram-positive model species differing from E. coli by a lower growth temperature optimum and a lower maximal growth rate. We show that, unlike in E. coli, there is little change in ribosome abundance for µ <0.4 h-1 in C. glutamicum and the fraction of active ribosomes is kept above 70% while the translation elongation rate declines 5-fold. Mathematical modelling indicates that the decrease in the translation elongation rate can be explained by a depletion of translation precursors.
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Affiliation(s)
- Susana Matamouros
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany.
| | - Thomas Gensch
- Institute of Biological Information Processing, IBI-1: Molecular and Cellular Physiology, Forschungszentrum Jülich, Jülich, Germany
| | - Martin Cerff
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany
| | - Christian C Sachs
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany
| | - Iman Abdollahzadeh
- Institute of Biological Information Processing, IBI-1: Molecular and Cellular Physiology, Forschungszentrum Jülich, Jülich, Germany
| | - Johnny Hendriks
- Institute of Biological Information Processing, IBI-1: Molecular and Cellular Physiology, Forschungszentrum Jülich, Jülich, Germany
| | - Lucas Horst
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany
| | - Niklas Tenhaef
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany
| | - Julia Tenhaef
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany
| | - Stephan Noack
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany
| | - Michaela Graf
- Institute of Biochemical Engineering, University of Stuttgart, Stuttgart, Germany
| | - Ralf Takors
- Institute of Biochemical Engineering, University of Stuttgart, Stuttgart, Germany
| | - Katharina Nöh
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany
| | - Michael Bott
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany.
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15
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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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16
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Miller KE, Vargas-Garcia C, Singh A, Moseley JB. The fission yeast cell size control system integrates pathways measuring cell surface area, volume, and time. Curr Biol 2023; 33:3312-3324.e7. [PMID: 37463585 PMCID: PMC10529673 DOI: 10.1016/j.cub.2023.06.054] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 06/01/2023] [Accepted: 06/20/2023] [Indexed: 07/20/2023]
Abstract
Eukaryotic cells tightly control their size, but the relevant aspect of size is unknown in most cases. Fission yeast divide at a threshold cell surface area (SA) due, in part, to the protein kinase Cdr2. We find that fission yeast cells only divide by SA under a size threshold. Mutants that divide at a larger size shift to volume-based divisions. Diploid cells divide at a larger size than haploid cells do, but they maintain SA-based divisions, and this indicates that the size threshold for changing from surface-area-based to volume-based control is set by ploidy. Within this size control system, we found that the mitotic activator Cdc25 accumulates like a volume-based sizer molecule, whereas the mitotic cyclin Cdc13 accumulates in the nucleus as a timer. We propose an integrated model for cell size control based on multiple signaling pathways that report on distinct aspects of cell size and growth, including cell SA (Cdr2), cell volume (Cdc25), and time (Cdc13). Combined modeling and experiments show how this system can generate both sizer- and adder-like properties.
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Affiliation(s)
- Kristi E Miller
- Department of Biochemistry and Cell Biology, The Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA
| | - Cesar Vargas-Garcia
- Grupo de Investigación en Sistemas Agropecuarios Sostenibles, Corporación Colombiana de Investigación Agropecuaria - AGROSAVIA, Bogotá 250047, Colombia
| | - Abhyudai Singh
- Department of Electrical and Computer Engineering, University of Delaware, Newark, DE 19716, USA
| | - James B Moseley
- Department of Biochemistry and Cell Biology, The Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA.
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17
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Ngo MC, Fujita Y, Suzuki T, Dung Do TM, Seki M, Nakayama T, Niihara K, Suematsu H. β-MoO 3 Whiskers in 99Mo/ 99mTc Radioisotope Production and 99Mo/ 99mTc Extraction Using Hot Atoms. Inorg Chem 2023; 62:13140-13147. [PMID: 37527499 DOI: 10.1021/acs.inorgchem.3c02125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/03/2023]
Abstract
β-MoO3 whiskers prepared by a thermal evaporation method and α-MoO3 particles were irradiated in a nuclear reactor to produce 99Mo/99mTc radioisotopes via neutron capture. The irradiated targets were then dispersed in water to extract the 99Mo/99mTc isotopes. Of the 99Mo formed in the β-MoO3 whiskers, 64.0 ± 7.4% was extracted with water; by contrast, only 8.8 ± 2.6% of the 99Mo formed in α-MoO3 was extracted. By comparing these data to the 98Mo concentration dissolved in water, we confirmed the hot-atom effect on both β-MoO3 whisker and α-MoO3 particle targets to transfer 99Mo isotopes from irradiated samples to water. In addition, the β-MoO3 whiskers exhibited a prominent hot-atom effect to transfer a higher ratio of 99Mo isotopes into water. To the best of our knowledge, this research is the first demonstration of β-MoO3 being used as an irradiation target in the neutron capture method. On the basis of the results, β-MoO3 is considered a promising irradiation target for producing 99Mo/99mTc by neutron capture and using water for the radioisotope extraction process in the future.
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Affiliation(s)
- Minh Chu Ngo
- Extreme Energy-Density Research Institute, Nagaoka University of Technology, Nagaoka, Niigata 940-2188, Japan
- Multi-Material Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Nagoya, Aichi 463-8560, Japan
- Faculty of International Training, Thai Nguyen University of Technology, Thai Nguyen 251750, Viet Nam
| | - Yoshitaka Fujita
- Department of JMTR, Japan Atomic Energy Agency, 4002 Narita, Oarai, Ibaraki 311-1393, Japan
| | - Tatsuya Suzuki
- Department of Nuclear System Safety Engineering, Nagaoka University of Technology, Nagaoka, Niigata 940-2188, Japan
| | - Thi Mai Dung Do
- Extreme Energy-Density Research Institute, Nagaoka University of Technology, Nagaoka, Niigata 940-2188, Japan
| | - Misaki Seki
- Department of JMTR, Japan Atomic Energy Agency, 4002 Narita, Oarai, Ibaraki 311-1393, Japan
| | - Tadachika Nakayama
- Extreme Energy-Density Research Institute, Nagaoka University of Technology, Nagaoka, Niigata 940-2188, Japan
| | - Koichi Niihara
- Extreme Energy-Density Research Institute, Nagaoka University of Technology, Nagaoka, Niigata 940-2188, Japan
| | - Hisayuki Suematsu
- Extreme Energy-Density Research Institute, Nagaoka University of Technology, Nagaoka, Niigata 940-2188, Japan
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18
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Composition and functions of bacterial membrane vesicles. Nat Rev Microbiol 2023:10.1038/s41579-023-00875-5. [PMID: 36932221 DOI: 10.1038/s41579-023-00875-5] [Citation(s) in RCA: 108] [Impact Index Per Article: 108.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/16/2023] [Indexed: 03/19/2023]
Abstract
Extracellular vesicles are produced by species across all domains of life, suggesting that vesiculation represents a fundamental principle of living matter. In Gram-negative bacteria, membrane vesicles (MVs) can originate either from blebs of the outer membrane or from endolysin-triggered explosive cell lysis, which is often induced by genotoxic stress. Although less is known about the mechanisms of vesiculation in Gram-positive and Gram-neutral bacteria, recent research has shown that both lysis and blebbing mechanisms also exist in these organisms. Evidence has accumulated over the past years that different biogenesis routes lead to distinct types of MV with varied structure and composition. In this Review, we discuss the different types of MV and their potential cargo packaging mechanisms. We summarize current knowledge regarding how MV composition determines their various functions including support of bacterial growth via the disposal of waste material, nutrient scavenging, export of bioactive molecules, DNA transfer, neutralization of phages, antibiotics and bactericidal functions, delivery of virulence factors and toxins to host cells and inflammatory and immunomodulatory effects. We also discuss the advantages of MV-mediated secretion compared with classic bacterial secretion systems and we introduce the concept of quantal secretion.
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19
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Kumar S, Karmacharya M, Cho YK. Bridging the Gap between Nonliving Matter and Cellular Life. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2202962. [PMID: 35988151 DOI: 10.1002/smll.202202962] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 07/28/2022] [Indexed: 06/15/2023]
Abstract
A cell, the fundamental unit of life, contains the requisite blueprint information necessary to survive and to build tissues, organs, and systems, eventually forming a fully functional living creature. A slight structural alteration can result in data misprinting, throwing the entire life process off balance. Advances in synthetic biology and cell engineering enable the predictable redesign of biological systems to perform novel functions. Individual functions and fundamental processes at the core of the biology of cells can be investigated by employing a synthetically constrained micro or nanoreactor. However, constructing a life-like structure from nonliving building blocks remains a considerable challenge. Chemical compartments, cascade signaling, energy generation, growth, replication, and adaptation within micro or nanoreactors must be comparable with their biological counterparts. Although these reactors currently lack the power and behavioral sophistication of their biological equivalents, their interface with biological systems enables the development of hybrid solutions for real-world applications, such as therapeutic agents, biosensors, innovative materials, and biochemical microreactors. This review discusses the latest advances in cell membrane-engineered micro or nanoreactors, as well as the limitations associated with high-throughput preparation methods and biological applications for the real-time modulation of complex pathological states.
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Affiliation(s)
- Sumit Kumar
- Center for Soft and Living Matter, Institute for Basic Science (IBS), UNIST-gil 50, Ulsan, 44919, Republic of Korea
- Department of Biomedical Engineering, Ulsan National Institute of Science and Technology (UNIST), UNIST-gil 50, Ulsan, 44919, Republic of Korea
| | - Mamata Karmacharya
- Center for Soft and Living Matter, Institute for Basic Science (IBS), UNIST-gil 50, Ulsan, 44919, Republic of Korea
- Department of Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), UNIST-gil 50, Ulsan, 44919, Republic of Korea
| | - Yoon-Kyoung Cho
- Center for Soft and Living Matter, Institute for Basic Science (IBS), UNIST-gil 50, Ulsan, 44919, Republic of Korea
- Department of Biomedical Engineering, Ulsan National Institute of Science and Technology (UNIST), UNIST-gil 50, Ulsan, 44919, Republic of Korea
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20
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Simas RG, Pessoa Junior A, Long PF. Mechanistic aspects of IPTG (isopropylthio-β-galactoside) transport across the cytoplasmic membrane of Escherichia coli-a rate limiting step in the induction of recombinant protein expression. J Ind Microbiol Biotechnol 2023; 50:kuad034. [PMID: 37849239 PMCID: PMC10639102 DOI: 10.1093/jimb/kuad034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Accepted: 10/16/2023] [Indexed: 10/19/2023]
Abstract
Coupling transcription of a cloned gene to the lac operon with induction by isopropylthio-β-galactoside (IPTG) has been a favoured approach for recombinant protein expression using Escherichia coli as a heterologous host for more than six decades. Despite a wealth of experimental data gleaned over this period, a quantitative relationship between extracellular IPTG concentration and consequent levels of recombinant protein expression remains surprisingly elusive across a broad spectrum of experimental conditions. This is because gene expression under lac operon regulation is tightly correlated with intracellular IPTG concentration due to allosteric regulation of the lac repressor protein (lacY). An in-silico mathematical model established that uptake of IPTG across the cytoplasmic membrane of E. coli by simple diffusion was negligible. Conversely, lacY mediated active transport was a rapid process, taking only some seconds for internal and external IPTG concentrations to equalize. Optimizing kcat and KM parameters by targeted mutation of the galactoside binding site in lacY could be a future strategy to improve the performance of recombinant protein expression. For example, if kcat were reduced whilst KM was increased, active transport of IPTG across the cytoplasmic membrane would be reduced, thereby lessening the metabolic burden on the cell and expediating accumulation of recombinant protein. The computational model described herein is made freely available and is amenable to optimize recombinant protein expression in other heterologous hosts. ONE-SENTENCE SUMMARY A computational model made freely available to optimize recombinant protein expression in Escherichia coli other heterologous hosts.
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Affiliation(s)
- Rodrigo G Simas
- Faculty of Life Sciences & Medicine, King's College London, 150 Stamford Street, London SE1 9NH, UK
- Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, Av. Prof. Lineu Prestes, 580, B16, 05508-000 São Paulo, SP, Brazil
| | - Adalberto Pessoa Junior
- Faculty of Life Sciences & Medicine, King's College London, 150 Stamford Street, London SE1 9NH, UK
- Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, Av. Prof. Lineu Prestes, 580, B16, 05508-000 São Paulo, SP, Brazil
| | - Paul F Long
- Faculty of Life Sciences & Medicine, King's College London, 150 Stamford Street, London SE1 9NH, UK
- Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, Av. Prof. Lineu Prestes, 580, B16, 05508-000 São Paulo, SP, Brazil
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21
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Zhu Y, Li D, Fan J, Zhang H, Eichhorn MP, Wang X, Yun T. A reinterpretation of the gap fraction of tree crowns from the perspectives of computer graphics and porous media theory. FRONTIERS IN PLANT SCIENCE 2023; 14:1109443. [PMID: 36814756 PMCID: PMC9939530 DOI: 10.3389/fpls.2023.1109443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Accepted: 01/09/2023] [Indexed: 06/18/2023]
Abstract
The gap fraction (GF) of vegetative canopies is an important property related to the contained bulk of reproductive elements and woody facets within the tree crown volume. This work was developed from the perspectives of porous media theory and computer graphics techniques, considering the vegetative elements in the canopy as a solid matrix and treating the gaps between them as pores to guide volume-based GFvol calculations. Woody components and individual leaves were extracted from terrestrial laser scanning data. The concept of equivalent leaf thickness describing the degrees of leaf curling and drooping was proposed to construct hexagonal prisms properly enclosing the scanned points of each leaf, and cylinder models were adopted to fit each branch segment, enabling the calculation of the equivalent leaf and branch volumes within the crown. Finally, the volume-based GFvol of the tree crown following the definition of the void fraction in porous media theory was calculated as one minus the ratio of the total plant leaf and branch volume to the canopy volume. This approach was tested on five tree species and a forest plot with variable canopy architecture, yielding an estimated maximum volume-based GFvol of 0.985 for a small crepe myrtle and a minimal volume-based GFvol of 0.953 for a sakura tree. The 3D morphology of each compositional element in the tree canopy was geometrically defined and the canopy was considered a porous structure to conduct GFvol calculations based on multidisciplinary theory.
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Affiliation(s)
- Yunfeng Zhu
- School of Information Science and Technology, Nanjing Forestry University, Nanjing, China
| | - Dongni Li
- School of Information Science and Technology, Nanjing Forestry University, Nanjing, China
| | - Jiangchuan Fan
- National Engineering Research Center for Information Technology in Agriculture, Beijing, China
| | - Huaiqing Zhang
- Research Institute of Forestry Resource Information Techniques, Chinese Academy of Forestry, Beijing, China
| | - Markus P. Eichhorn
- School of Biological, Earth and Environmental Sciences, University College Cork, Cork, Ireland
- Environmental Research Institute, University College Cork, Cork, Ireland
| | - Xiangjun Wang
- Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Ting Yun
- School of Information Science and Technology, Nanjing Forestry University, Nanjing, China
- Forestry College, Nanjing Forestry University, Nanjing, China
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22
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Looney DP, Potter AW, Arcidiacono DM, Santee WR, Friedl KE. Body surface area equations for physically active men and women. Am J Hum Biol 2023; 35:e23823. [PMID: 36285812 DOI: 10.1002/ajhb.23823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 09/26/2022] [Accepted: 10/03/2022] [Indexed: 11/11/2022] Open
Abstract
OBJECTIVES To improve predictive formulae for estimating body surface area (BSA) in healthy men and women using a modern three-dimensional scanner technology. METHODS Body surface areas were obtained from a convenience sample of 1267 US Marines (464 women and 803 men) using a whole body surface scanner (Size Stream SS20). The reliability of SS20 measures of total and regional BSA within participants was compared across triplicate scans. We then derived a series of formulae to estimate SS20-measured BSA using various combinations of sex, height, and mass. We also assessed relationships between percent body fat measured by dual-energy x-ray absorptiometry and sex-specific formulae errors in Marines. RESULTS Body surface areas recorded by the SS20 were highly reliable whether measured for the total body or by region (ICC ≥ .962). Formulae estimates of BSA from sex, height, and mass were precise (root-mean-square deviation, 0.031 m2 ). Errors from the Marine Corps formulae were positively associated with percent body fat for men (p = .001) but not women (p = .843). CONCLUSIONS Clinicians, military leaders, and researchers can use the newly developed BSA formulae for precise estimates in healthy physically active men and women. Users should be aware that height- and mass-based BSA estimates are less accurate for individuals with extremely low or high percent body fat.
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Affiliation(s)
- David P Looney
- Military Performance Division, United States Army Research Institute of Environmental Medicine (USARIEM), Natick, Massachusetts, USA
| | - Adam W Potter
- Thermal and Mountain Medicine Division, USARIEM, Natick, Massachusetts, USA
| | - Danielle M Arcidiacono
- Military Performance Division, United States Army Research Institute of Environmental Medicine (USARIEM), Natick, Massachusetts, USA.,Oak Ridge Institute for Science and Education (ORISE), Oak Ridge, Tennessee, USA
| | - William R Santee
- Military Performance Division, United States Army Research Institute of Environmental Medicine (USARIEM), Natick, Massachusetts, USA
| | - Karl E Friedl
- Office of the Senior Scientist, USARIEM, Natick, Massachusetts, USA
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23
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Cayron J, Dedieu-Berne A, Lesterlin C. Bacterial filaments recover by successive and accelerated asymmetric divisions that allow rapid post-stress cell proliferation. Mol Microbiol 2023; 119:237-251. [PMID: 36527185 DOI: 10.1111/mmi.15016] [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: 07/19/2022] [Revised: 12/09/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022]
Abstract
Filamentation is a reversible morphological change triggered in response to various stresses that bacteria might encounter in the environment, during host infection or antibiotic treatments. Here we re-visit the dynamics of filament formation and recovery using a consistent framework based on live-cells microscopy. We compare the fate of filamentous Escherichia coli induced by cephalexin that inhibits cell division or by UV-induced DNA-damage that additionally perturbs chromosome segregation. We show that both filament types recover by successive and accelerated rounds of divisions that preferentially occur at the filaments' tip, thus resulting in the rapid production of multiple daughter cells with tightly regulated size. The DNA content, viability and further division of the daughter cells essentially depends on the coordination between chromosome segregation and division within the mother filament. Septum positioning at the filaments' tip depends on the Min system, while the nucleoid occlusion protein SlmA regulates the timing of division to prevent septum closure on unsegregated chromosomes. Our results not only recapitulate earlier conclusions but provide a higher level of detail regarding filaments division and the fate of the daughter cells. Together with previous reports, this work uncovers how filamentation recovery allows for a rapid cell proliferation after stress treatment.
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Affiliation(s)
- Julien Cayron
- Microbiologie Moléculaire et Biochimie Structurale (MMSB), Université Lyon 1, CNRS, Inserm, UMR5086, Lyon, France
| | - Annick Dedieu-Berne
- Microbiologie Moléculaire et Biochimie Structurale (MMSB), Université Lyon 1, CNRS, Inserm, UMR5086, Lyon, France
| | - Christian Lesterlin
- Microbiologie Moléculaire et Biochimie Structurale (MMSB), Université Lyon 1, CNRS, Inserm, UMR5086, Lyon, France
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24
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Weber A, Gibisch M, Tyrakowski D, Cserjan-Puschmann M, Toca-Herrera JL, Striedner G. Recombinant Peptide Production Softens Escherichia coli Cells and Increases Their Size during C-Limited Fed-Batch Cultivation. Int J Mol Sci 2023; 24:2641. [PMID: 36768962 PMCID: PMC9916741 DOI: 10.3390/ijms24032641] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 01/25/2023] [Accepted: 01/25/2023] [Indexed: 02/03/2023] Open
Abstract
Stress-associated changes in the mechanical properties at the single-cell level of Escherichia coli (E. coli) cultures in bioreactors are still poorly investigated. In our study, we compared peptide-producing and non-producing BL21(DE3) cells in a fed-batch cultivation with tightly controlled process parameters. The cell growth, peptide content, and cell lysis were analysed, and changes in the mechanical properties were investigated using atomic force microscopy. Recombinant-tagged somatostatin-28 was expressed as soluble up to 197 ± 11 mg g-1. The length of both cultivated strains increased throughout the cultivation by up to 17.6%, with nearly constant diameters. The peptide-producing cells were significantly softer than the non-producers throughout the cultivation, and respective Young's moduli decreased by up to 57% over time. A minimum Young's modulus of 1.6 MPa was observed after 23 h of the fed-batch. Furthermore, an analysis of the viscoelastic properties revealed that peptide-producing BL21(DE3) appeared more fluid-like and softer than the non-producing reference. For the first time, we provide evidence that the physical properties (i.e., the mechanical properties) on the single-cell level are significantly influenced by the metabolic burden imposed by the recombinant peptide expression and C-limitation in bioreactors.
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Affiliation(s)
- Andreas Weber
- Christian Doppler Laboratory for Production of Next-Level Biopharmaceuticals in E. coli, Institute of Bioprocess Science and Engineering, Department of Biotechnology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
- Institute of Biophysics, Department of Bionanosciences, University of Natural Resources and Life Sciences, Muthgasse 11, 1190 Vienna, Austria
| | - Martin Gibisch
- Christian Doppler Laboratory for Production of Next-Level Biopharmaceuticals in E. coli, Institute of Bioprocess Science and Engineering, Department of Biotechnology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
| | - Daniel Tyrakowski
- Institute of Biophysics, Department of Bionanosciences, University of Natural Resources and Life Sciences, Muthgasse 11, 1190 Vienna, Austria
| | - Monika Cserjan-Puschmann
- Christian Doppler Laboratory for Production of Next-Level Biopharmaceuticals in E. coli, Institute of Bioprocess Science and Engineering, Department of Biotechnology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
| | - José L. Toca-Herrera
- Institute of Biophysics, Department of Bionanosciences, University of Natural Resources and Life Sciences, Muthgasse 11, 1190 Vienna, Austria
| | - Gerald Striedner
- Christian Doppler Laboratory for Production of Next-Level Biopharmaceuticals in E. coli, Institute of Bioprocess Science and Engineering, Department of Biotechnology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
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25
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Serbanescu D, Ojkic N, Banerjee S. Cellular resource allocation strategies for cell size and shape control in bacteria. FEBS J 2022; 289:7891-7906. [PMID: 34665933 PMCID: PMC9016100 DOI: 10.1111/febs.16234] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 09/21/2021] [Accepted: 10/18/2021] [Indexed: 01/14/2023]
Abstract
Bacteria are highly adaptive microorganisms that thrive in a wide range of growth conditions via changes in cell morphologies and macromolecular composition. How bacterial morphologies are regulated in diverse environmental conditions is a long-standing question. Regulation of cell size and shape implies control mechanisms that couple the growth and division of bacteria to their cellular environment and macromolecular composition. In the past decade, simple quantitative laws have emerged that connect cell growth to proteomic composition and the nutrient availability. However, the relationships between cell size, shape, and growth physiology remain challenging to disentangle and unifying models are lacking. In this review, we focus on regulatory models of cell size control that reveal the connections between bacterial cell morphology and growth physiology. In particular, we discuss how changes in nutrient conditions and translational perturbations regulate the cell size, growth rate, and proteome composition. Integrating quantitative models with experimental data, we identify the physiological principles of bacterial size regulation, and discuss the optimization strategies of cellular resource allocation for size control.
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Affiliation(s)
- Diana Serbanescu
- Department of Physics and Astronomy, University College London, UK
| | - Nikola Ojkic
- Department of Physics and Astronomy, University College London, UK
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26
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Cylke KC, Si F, Banerjee S. Effects of antibiotics on bacterial cell morphology and their physiological origins. Biochem Soc Trans 2022; 50:1269-1279. [PMID: 36093840 PMCID: PMC10152891 DOI: 10.1042/bst20210894] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Revised: 08/05/2022] [Accepted: 08/17/2022] [Indexed: 11/17/2022]
Abstract
Characterizing the physiological response of bacterial cells to antibiotic treatment is crucial for the design of antibacterial therapies and for understanding the mechanisms of antibiotic resistance. While the effects of antibiotics are commonly characterized by their minimum inhibitory concentrations or the minimum bactericidal concentrations, the effects of antibiotics on cell morphology and physiology are less well characterized. Recent technological advances in single-cell studies of bacterial physiology have revealed how different antibiotic drugs affect the physiological state of the cell, including growth rate, cell size and shape, and macromolecular composition. Here, we review recent quantitative studies on bacterial physiology that characterize the effects of antibiotics on bacterial cell morphology and physiological parameters. In particular, we present quantitative data on how different antibiotic targets modulate cellular shape metrics including surface area, volume, surface-to-volume ratio, and the aspect ratio. Using recently developed quantitative models, we relate cell shape changes to alterations in the physiological state of the cell, characterized by changes in the rates of cell growth, protein synthesis and proteome composition. Our analysis suggests that antibiotics induce distinct morphological changes depending on their cellular targets, which may have important implications for the regulation of cellular fitness under stress.
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Affiliation(s)
- K. Callaghan Cylke
- Department of Physics, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Fangwei Si
- Department of Physics, Carnegie Mellon University, Pittsburgh, PA 15213, USA
- The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Shiladitya Banerjee
- Department of Physics, Carnegie Mellon University, Pittsburgh, PA 15213, USA
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27
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Even allocation of benefits stabilizes microbial community engaged in metabolic division of labor. Cell Rep 2022; 40:111410. [PMID: 36170826 DOI: 10.1016/j.celrep.2022.111410] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 07/10/2022] [Accepted: 09/02/2022] [Indexed: 11/21/2022] Open
Abstract
Microbial communities execute metabolic pathways to drive global nutrient cycles. Within a community, functionally specialized strains can perform different yet complementary steps within a linear pathway, a phenomenon termed metabolic division of labor (MDOL). However, little is known about how such metabolic behaviors shape microbial communities. Here, we derive a theoretical framework to define the assembly of a community that degrades an organic compound through MDOL. The framework indicates that to ensure community stability, the strains performing the initial steps should hold a growth advantage (m) over the "private benefit" (n) of the strain performing the last step. The steady-state frequency of the last strain is then determined by the quotient of n and m. Our experiments show that the framework accurately predicts the assembly of our synthetic consortia that degrade naphthalene through MDOL. Our results provide insights for designing and managing stable microbial systems for metabolic pathway optimization.
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28
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Pacey EK, Maherali H, Husband BC. Polyploidy increases storage but decreases structural stability in Arabidopsis thaliana. Curr Biol 2022; 32:4057-4063.e3. [PMID: 35944542 DOI: 10.1016/j.cub.2022.07.019] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 05/05/2022] [Accepted: 07/08/2022] [Indexed: 11/26/2022]
Abstract
Whole-genome duplication, leading to polyploidy and endopolyploidy, is widespread throughout the tree of life.1-3 Both polyploidy and endopolyploidy can increase cell size via nucleotypic effects, but the phenotypic consequences of increased cell size at the tissue and whole-organism levels are less well understood.1-4 We quantified the consequences of autopolyploidy and endopolyploidy in nine diploid accessions of Arabidopsis thaliana, representing a gradient in endopolyploidy, to their corresponding experimentally synthesized neo-tetraploid and neo-octoploid cytotypes. The increase in cell size following genome duplication increased plant storage capacity, which increased tolerance of resource limitation, but also incurred biomechanical costs because of a reduction in the amount of cell wall per unit tissue volume. Our findings also show that the functional consequences of autopolyploidy can vary with accession identity, and the presence of this variation suggests that there is potential for adaptation following whole-genome duplication.
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Affiliation(s)
- Evan K Pacey
- Department of Integrative Biology, University of Guelph, 50 Stone Road E., Guelph, ON N1G 2W1, Canada
| | - Hafiz Maherali
- Department of Integrative Biology, University of Guelph, 50 Stone Road E., Guelph, ON N1G 2W1, Canada
| | - Brian C Husband
- Department of Integrative Biology, University of Guelph, 50 Stone Road E., Guelph, ON N1G 2W1, Canada.
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29
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Yin Q, Sun Y, Li B, Feng Z, Wu G. The r/K selection theory and its application in biological wastewater treatment processes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 824:153836. [PMID: 35176382 DOI: 10.1016/j.scitotenv.2022.153836] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 01/23/2022] [Accepted: 02/08/2022] [Indexed: 06/14/2023]
Abstract
Understanding the characteristics of functional organisms is the key to managing and updating biological processes for wastewater treatment. This review, for the first time, systematically characterized two typical types of strategists in wastewater treatment ecosystems via the r/K selection theory and provided novel strategies for selectively enriching microbial community. Functional organisms involved in nitrification (e.g., Nitrosomonas and Nitrosococcus), anammox (Candidatus Brocadia), and methanogenesis (Methanosarcinaceae) are identified as r-strategists with fast growth capacities and low substrate affinities. These r-strategists can achieve high pollutant removal loading rates. On the other hand, other organisms such as Nitrosospira spp., Candidatus Kuenenia, and Methanosaetaceae, are characterized as K-strategists with slow growth rates but high substrate affinities, which can decrease the pollutant concentration to low levels. More importantly, K-strategists may play crucial roles in the biodegradation of recalcitrant organic pollutants. The food-to-microorganism ratio, mass transfer, cell size, and biomass morphology are the key factors determining the selection of r-/K-strategists. These factors can be related with operating parameters (e.g., solids and hydraulic retention time), biomass morphology (biofilm or granules), and operating modes (continuous-flow or sequencing batch), etc., to achieve the efficient acclimation of targeted r-/K-strategists. For practical applications, the concept of substrate flux was put forward to further benefit the selective enrichment of r-/K-strategists, fulfilling effective management and improvement of engineered pollution control bioprocesses. Finally, the future perspectives regarding the development of the r/K selection theory in wastewater treatment processes were discussed.
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Affiliation(s)
- Qidong Yin
- College of Science and Engineering, National University of Ireland, Galway, Galway H91 TK33, Ireland; Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, Guangdong, China
| | - Yuepeng Sun
- Department of Civil and Environmental Engineering, Virginia Tech, Ashburn, VA 20147, United States
| | - Bo Li
- Department of Civil & Environmental Engineering, University of Washington, Seattle, WA 98105, United States
| | - Zhaolu Feng
- Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, Guangdong, China
| | - Guangxue Wu
- College of Science and Engineering, National University of Ireland, Galway, Galway H91 TK33, Ireland.
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30
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Cooper ZS, Rapp JZ, Shoemaker AMD, Anderson RE, Zhong ZP, Deming JW. Evolutionary Divergence of Marinobacter Strains in Cryopeg Brines as Revealed by Pangenomics. Front Microbiol 2022; 13:879116. [PMID: 35733954 PMCID: PMC9207381 DOI: 10.3389/fmicb.2022.879116] [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: 02/18/2022] [Accepted: 05/05/2022] [Indexed: 11/30/2022] Open
Abstract
Marinobacter spp. are cosmopolitan in saline environments, displaying a diverse set of metabolisms that allow them to competitively occupy these environments, some of which can be extreme in both salinity and temperature. Here, we introduce a distinct cluster of Marinobacter genomes, composed of novel isolates and in silico assembled genomes obtained from subzero, hypersaline cryopeg brines, relic seawater-derived liquid habitats within permafrost sampled near Utqiaġvik, Alaska. Using these new genomes and 45 representative publicly available genomes of Marinobacter spp. from other settings, we assembled a pangenome to examine how the new extremophile members fit evolutionarily and ecologically, based on genetic potential and environmental source. This first genus-wide genomic analysis revealed that Marinobacter spp. in general encode metabolic pathways that are thermodynamically favored at low temperature, cover a broad range of organic compounds, and optimize protein usage, e.g., the Entner–Doudoroff pathway, the glyoxylate shunt, and amino acid metabolism. The new isolates contributed to a distinct clade of subzero brine-dwelling Marinobacter spp. that diverged genotypically and phylogenetically from all other Marinobacter members. The subzero brine clade displays genomic characteristics that may explain competitive adaptations to the extreme environments they inhabit, including more abundant membrane transport systems (e.g., for organic substrates, compatible solutes, and ions) and stress-induced transcriptional regulatory mechanisms (e.g., for cold and salt stress) than in the other Marinobacter clades. We also identified more abundant signatures of potential horizontal transfer of genes involved in transcription, the mobilome, and a variety of metabolite exchange systems, which led to considering the importance of this evolutionary mechanism in an extreme environment where adaptation via vertical evolution is physiologically rate limited. Assessing these new extremophile genomes in a pangenomic context has provided a unique view into the ecological and evolutionary history of the genus Marinobacter, particularly with regard to its remarkable diversity and its opportunism in extremely cold and saline environments.
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Affiliation(s)
- Zachary S. Cooper
- School of Oceanography, University of Washington, Seattle, WA, United States
- Astrobiology Program, University of Washington, Seattle, WA, United States
- *Correspondence: Zachary S. Cooper, , orcid.org/0000-0001-6515-7971
| | - Josephine Z. Rapp
- Department of Biochemistry, Microbiology and Bioinformatics, Université Laval, Québec, QC, Canada
- Center for Northern Studies (CEN), Université Laval, Québec, QC, Canada
- Institute of Integrative Biology and Systems (IBIS), Université Laval, Québec, QC, Canada
| | - Anna M. D. Shoemaker
- Department of Earth Sciences, Montana State University, Bozeman, MT, United States
| | - Rika E. Anderson
- Department of Biology, Carleton College, Northfield, MN, United States
| | - Zhi-Ping Zhong
- Byrd Polar and Climate Research Center, Ohio State University, Columbus, OH, United States
- Department of Microbiology, Ohio State University, Columbus, OH, United States
- Center of Microbiome Science, Ohio State University, Columbus, OH, United States
| | - Jody W. Deming
- School of Oceanography, University of Washington, Seattle, WA, United States
- Astrobiology Program, University of Washington, Seattle, WA, United States
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Abstract
Bacteria have evolved to develop multiple strategies for antibiotic resistance by effectively reducing intracellular antibiotic concentrations or antibiotic binding affinities, but the role of cell morphology in antibiotic resistance remains poorly understood. By analyzing cell morphological data for different bacterial species under antibiotic stress, we find that bacteria increase or decrease the cell surface-to-volume ratio depending on the antibiotic target. Using quantitative modeling, we show that by reducing the surface-to-volume ratio, bacteria can effectively reduce the intracellular antibiotic concentration by decreasing antibiotic influx. The model further predicts that bacteria can increase the surface-to-volume ratio to induce the dilution of membrane-targeting antibiotics, in agreement with experimental data. Using a whole-cell model for the regulation of cell shape and growth by antibiotics, we predict shape transformations that bacteria can utilize to increase their fitness in the presence of antibiotics. We conclude by discussing additional pathways for antibiotic resistance that may act in synergy with shape-induced resistance.
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32
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Ivshina I, Bazhutin G, Tyan S, Polygalov M, Subbotina M, Tyumina E. Cellular Modifications of Rhodococci Exposed to Separate and Combined Effects of Pharmaceutical Pollutants. Microorganisms 2022; 10:microorganisms10061101. [PMID: 35744619 PMCID: PMC9227840 DOI: 10.3390/microorganisms10061101] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 05/23/2022] [Accepted: 05/23/2022] [Indexed: 01/10/2023] Open
Abstract
Actinomycetes of the genus Rhodococcus (class Actinomycetia) are dominant dwellers of biotopes with anthropogenic load. They serve as a natural system of primary response to xenobiotics in open ecosystems, initiate defensive responses in the presence of pollutants, and are regarded as ideal agents capable of transforming and degrading pharmaceuticals. Here, the ability of selected Rhodococcus strains to co-metabolize nonsteroidal anti-inflammatory drugs (ibuprofen, meloxicam, and naproxen) and information on the protective mechanisms of rhodococci against toxic effects of pharmaceuticals, individually or in a mixture, have been demonstrated. For the first time, R. ruber IEGM 439 provided complete decomposition of 100 mg/L meloxicam after seven days. It was shown that versatile cellular modifications occurring at the early development stages of nonspecific reactions of Rhodococcus spp. in response to separate and combined effects of the tested pharmaceuticals included changes in electrokinetic characteristics and catalase activity; transition from unicellular to multicellular life forms accompanied by pronounced morphological abnormalities; changes in the average size of vegetative cells and surface area-to-volume ratio; and the formation of linked cell assemblages. The obtained data are considered as adaptation mechanisms in rhodococci, and consequently their increased resistance to separate and combined effects of ibuprofen, meloxicam, and naproxen.
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Affiliation(s)
- Irina Ivshina
- Perm Federal Research Center Ural Branch Russian Academy of Sciences, 13a Lenin Street, 614990 Perm, Russia; (G.B.); (M.P.); (M.S.); (E.T.)
- Department of Microbiology and Immunology, Perm State National Research University, 15 Bukirev Street, 614990 Perm, Russia;
- Correspondence:
| | - Grigory Bazhutin
- Perm Federal Research Center Ural Branch Russian Academy of Sciences, 13a Lenin Street, 614990 Perm, Russia; (G.B.); (M.P.); (M.S.); (E.T.)
- Department of Microbiology and Immunology, Perm State National Research University, 15 Bukirev Street, 614990 Perm, Russia;
| | - Semyon Tyan
- Department of Microbiology and Immunology, Perm State National Research University, 15 Bukirev Street, 614990 Perm, Russia;
| | - Maxim Polygalov
- Perm Federal Research Center Ural Branch Russian Academy of Sciences, 13a Lenin Street, 614990 Perm, Russia; (G.B.); (M.P.); (M.S.); (E.T.)
- Department of Microbiology and Immunology, Perm State National Research University, 15 Bukirev Street, 614990 Perm, Russia;
| | - Maria Subbotina
- Perm Federal Research Center Ural Branch Russian Academy of Sciences, 13a Lenin Street, 614990 Perm, Russia; (G.B.); (M.P.); (M.S.); (E.T.)
- Department of Microbiology and Immunology, Perm State National Research University, 15 Bukirev Street, 614990 Perm, Russia;
| | - Elena Tyumina
- Perm Federal Research Center Ural Branch Russian Academy of Sciences, 13a Lenin Street, 614990 Perm, Russia; (G.B.); (M.P.); (M.S.); (E.T.)
- Department of Microbiology and Immunology, Perm State National Research University, 15 Bukirev Street, 614990 Perm, Russia;
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Czerwińska-Główka D, Skonieczna M, Barylski A, Golba S, Przystaś W, Zabłocka-Godlewska E, Student S, Cwalina B, Krukiewicz K. Bifunctional conducting polymer matrices with antibacterial and neuroprotective effects. Bioelectrochemistry 2022; 144:108030. [PMID: 34896782 DOI: 10.1016/j.bioelechem.2021.108030] [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: 08/23/2021] [Revised: 10/24/2021] [Accepted: 11/29/2021] [Indexed: 11/02/2022]
Abstract
Current trends in the field of neural tissue engineering include the design of advanced biomaterials combining excellent electrochemical performance with versatile biological characteristics. The purpose of this work was to develop an antibacterial and neuroprotective coating based on a conducting polymer - poly(3,4-ethylenedioxypyrrole) (PEDOP), loaded with an antibiotic agent - tetracycline (Tc). Employing an electrochemical technique to immobilize Tc within a growing polymer matrix allowed to fabricate robust PEDOP/Tc coatings with a high charge storage capacity (63.65 ± 6.05 mC/cm2), drug release efficiency (629.4 µg/cm2 ± 62.7 µg/cm2), and low charge transfer resistance (2.4 ± 0.1 kΩ), able to deliver a stable electrical signal. PEDOP/Tc were found to exhibit strong antimicrobial effects against Gram-negative bacteria Escherichia coli, expressed through negligible adhesion, reduction in viability, and a characteristic elongation of bacterial cells. Cytocompatibility and neuroprotective effects were evaluated using a rat neuroblastoma B35 cell line, and were analyzed using MTT, cell cycle, and Annexin-V apoptosis assays. The presence of Tc was found to enhance neural cell viability and neurite outgrowth. The results confirmed that PEDOP/Tc can serve as an efficient neural electrode coating able to enhance charge transfer, as well as to exhibit bifunctional biological characteristics, different for eukaryotic and prokaryotic cells.
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Affiliation(s)
- Dominika Czerwińska-Główka
- Department of Physical Chemistry and Technology of Polymers, Silesian University of Technology, M.Strzody 9, 44-100 Gliwice, Poland
| | - Magdalena Skonieczna
- Department of Systems Biology and Engineering, Faculty of Automatic Control, Electronics and Computer Science, Silesian University of Technology, Akademicka 16, 44-100 Gliwice, Poland; Biotechnology Centre, Silesian University of Technology, B. Krzywoustego 8, 44-100 Gliwice, Poland
| | - Adrian Barylski
- Institute of Materials Engineering, University of Silesia, 75 Pulku Piechoty, 41-500 Chorzow, Poland
| | - Sylwia Golba
- Institute of Materials Engineering, University of Silesia, 75 Pulku Piechoty, 41-500 Chorzow, Poland
| | - Wioletta Przystaś
- Biotechnology Centre, Silesian University of Technology, B. Krzywoustego 8, 44-100 Gliwice, Poland; Department of Air Protection, Faculty of Energy and Environmental Engineering, Silesian University of Technology, S. Konarskiego 22B, 44-100 Gliwice, Poland
| | - Ewa Zabłocka-Godlewska
- Biotechnology Centre, Silesian University of Technology, B. Krzywoustego 8, 44-100 Gliwice, Poland; Department of Air Protection, Faculty of Energy and Environmental Engineering, Silesian University of Technology, S. Konarskiego 22B, 44-100 Gliwice, Poland
| | - Sebastian Student
- Department of Systems Biology and Engineering, Faculty of Automatic Control, Electronics and Computer Science, Silesian University of Technology, Akademicka 16, 44-100 Gliwice, Poland; Biotechnology Centre, Silesian University of Technology, B. Krzywoustego 8, 44-100 Gliwice, Poland
| | - Beata Cwalina
- Biotechnology Centre, Silesian University of Technology, B. Krzywoustego 8, 44-100 Gliwice, Poland; Department of Environmental Biotechnology, Faculty of Energy and Environmental Engineering, Silesian University of Technology, S.Konarskiego 18, 44-100 Gliwice, Poland
| | - Katarzyna Krukiewicz
- Department of Physical Chemistry and Technology of Polymers, Silesian University of Technology, M.Strzody 9, 44-100 Gliwice, Poland.
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Elementary vectors and autocatalytic sets for resource allocation in next-generation models of cellular growth. PLoS Comput Biol 2022; 18:e1009843. [PMID: 35104290 PMCID: PMC8853647 DOI: 10.1371/journal.pcbi.1009843] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 02/17/2022] [Accepted: 01/18/2022] [Indexed: 11/19/2022] Open
Abstract
Traditional (genome-scale) metabolic models of cellular growth involve an approximate biomass “reaction”, which specifies biomass composition in terms of precursor metabolites (such as amino acids and nucleotides). On the one hand, biomass composition is often not known exactly and may vary drastically between conditions and strains. On the other hand, the predictions of computational models crucially depend on biomass. Also elementary flux modes (EFMs), which generate the flux cone, depend on the biomass reaction. To better understand cellular phenotypes across growth conditions, we introduce and analyze new classes of elementary vectors for comprehensive (next-generation) metabolic models, involving explicit synthesis reactions for all macromolecules. Elementary growth modes (EGMs) are given by stoichiometry and generate the growth cone. Unlike EFMs, they are not support-minimal, in general, but cannot be decomposed “without cancellations”. In models with additional (capacity) constraints, elementary growth vectors (EGVs) generate a growth polyhedron and depend also on growth rate. However, EGMs/EGVs do not depend on the biomass composition. In fact, they cover all possible biomass compositions and can be seen as unbiased versions of elementary flux modes/vectors (EFMs/EFVs) used in traditional models. To relate the new concepts to other branches of theory, we consider autocatalytic sets of reactions. Further, we illustrate our results in a small model of a self-fabricating cell, involving glucose and ammonium uptake, amino acid and lipid synthesis, and the expression of all enzymes and the ribosome itself. In particular, we study the variation of biomass composition as a function of growth rate. In agreement with experimental data, low nitrogen uptake correlates with high carbon (lipid) storage. Next-generation, genome-scale metabolic models allow to study the reallocation of cellular resources upon changing environmental conditions, by not only modeling flux distributions, but also expression profiles of the catalyzing proteome. In particular, they do no longer assume a fixed biomass composition. Methods to identify optimal solutions in such comprehensive models exist, however, an unbiased understanding of all feasible allocations is missing so far. Here we develop new concepts, called elementary growth modes and vectors, that provide a generalized definition of minimal pathways, thereby extending classical elementary flux modes (used in traditional models with a fixed biomass composition). The new concepts provide an understanding of all possible flux distributions and of all possible biomass compositions. In other words, elementary growth modes and vectors are the unique functional units in any comprehensive model of cellular growth. As an example, we show that lipid accumulation upon nitrogen starvation is a consequence of resource allocation and does not require active regulation. Our work puts current approaches on a theoretical basis and allows to seamlessly transfer existing workflows (e.g. for the design of cell factories) to next-generation metabolic models.
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A Novel 3D Titanium Surface Produced by Selective Laser Sintering to Counteract Streptococcus oralis Biofilm Formation. APPLIED SCIENCES-BASEL 2021. [DOI: 10.3390/app112411915] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The topography of implant surfaces influences the interaction relationship between material and bacteria. The aim of this work was to characterize a novel 3D titanium surface, produced using Selective Laser Sintering (SLS), and to compare the bacterial interaction with machined and double acid etching (DAE) discs. The surface was characterized by atomic force microscopy (AFM), scanning electron microscopy (SEM), and Energy Dispersive X-ray Spectrometry (EDX). The wettability was measured using the sessile method. The microbiological investigation consisted in the cultivation of a bacterial pioneer, Streptococcus oralis, on titanium surfaces, previously covered by human saliva in order to form the acquired pellicle. Then, colony forming units (CFUs), biofilm biomass quantification, analyses of viable and dead cells, and SEM observation were determined after 24 h of S. oralis biofilm formation on the different discs. A significantly higher nano-roughness with respect to the other two groups characterized the novel 3D surface, but the wettability was similar to that of machined samples. The microbiological assays demonstrated that the 3D discs reported significantly lower values of CFUs and biofilm biomass with respect to machined surfaces; however, no significant differences were found with the DAE surfaces. The live/dead staining confirmed the lower percentage of living cells on DAE and 3D surfaces compared with the machined. This novel 3D surface produced by SLS presented a high antiadhesive and antibiofilm activity.
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36
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Czerwińska-Główka D, Krukiewicz K. Guidelines for a Morphometric Analysis of Prokaryotic and Eukaryotic Cells by Scanning Electron Microscopy. Cells 2021; 10:3304. [PMID: 34943812 PMCID: PMC8699492 DOI: 10.3390/cells10123304] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 11/11/2021] [Accepted: 11/24/2021] [Indexed: 11/17/2022] Open
Abstract
The invention of a scanning electron microscopy (SEM) pushed the imaging methods and allowed for the observation of cell details with a high resolution. Currently, SEM appears as an extremely useful tool to analyse the morphology of biological samples. The aim of this paper is to provide a set of guidelines for using SEM to analyse morphology of prokaryotic and eukaryotic cells, taking as model cases Escherichia coli bacteria and B-35 rat neuroblastoma cells. Herein, we discuss the necessity of a careful sample preparation and provide an optimised protocol that allows to observe the details of cell ultrastructure (≥ 50 nm) with a minimum processing effort. Highlighting the versatility of morphometric descriptors, we present the most informative parameters and couple them with molecular processes. In this way, we indicate the wide range of information that can be collected through SEM imaging of biological materials that makes SEM a convenient screening method to detect cell pathology.
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Affiliation(s)
| | - Katarzyna Krukiewicz
- Department of Physical Chemistry and Technology of Polymers, Silesian University of Technology, 44-100 Gliwice, Poland;
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37
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Choi J, Patil A, Vendrow E, Touponse G, Aboukhater L, Forrester JD, Spain DA. Practical Computer Vision Application to Compute Total Body Surface Area Burn: Reappraising a Fundamental Burn Injury Formula in the Modern Era. JAMA Surg 2021; 157:129-135. [PMID: 34817552 DOI: 10.1001/jamasurg.2021.5848] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Importance Critical burn management decisions rely on accurate percent total body surface area (%TBSA) burn estimation. Existing %TBSA burn estimation models (eg, Lund-Browder chart and rule of nines) were derived from a linear formula and a limited number of individuals a century ago and do not reflect the range of body habitus of the modern population. Objective To develop a practical %TBSA burn estimation tool that accounts for exact burn injury pattern, sex, and body habitus. Design, Setting, and Participants This population-based cohort study evaluated the efficacy of a computer vision algorithm application in processing an adult laser body scan data set. High-resolution surface anthropometry laser body scans of 3047 North American and European adults aged 18 to 65 years from the Civilian American and European Surface Anthropometry Resource data set (1998-2001) were included. Of these, 1517 participants (49.8%) were male. Race and ethnicity data were not available for analysis. Analyses were conducted in 2020. Main Outcomes and Measures The contributory %TBSA for 18 body regions in each individual. Mobile application for real-time %TBSA burn computation based on sex, habitus, and exact burn injury pattern. Results Of the 3047 individuals aged 18 to 65 years for whom body scans were available, 1517 (49.8%) were male. Wide individual variability was found in the extent to which major body regions contributed to %TBSA, especially in the torso and legs. Anterior torso %TBSA increased with increasing body habitus (mean [SD], 15.1 [0.9] to 19.1 [2.0] for male individuals; 15.1 [0.8] to 18.0 [1.7] for female individuals). This increase was attributable to increase in abdomen %TBSA (mean [SD], 5.3 [0.7] to 8.7 [1.8]) among male individuals and increase in abdomen (mean [SD], 4.6 [0.6] to 6.8 [1.7]) and pelvis (mean [SD], 1.5 [0.2] to 2.9 [0.9]) %TBSAs among female individuals. For most body regions, Lund-Browder chart and rule of nines estimates fell outside the population's measured interquartile ranges. The mobile application tested in this study, Burn Area, facilitated accurate %TBSA burn computation based on exact burn injury pattern for 10 sex and body habitus-specific models. Conclusions and Relevance Computer vision algorithm application to a large laser body scan data set may provide a practical tool that facilitates accurate %TBSA burn computation in the modern era.
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Affiliation(s)
- Jeff Choi
- Department of Surgery, Stanford University, Stanford, California.,Surgeons Writing About Trauma, Stanford University, Stanford, California
| | - Advait Patil
- Surgeons Writing About Trauma, Stanford University, Stanford, California.,Department of Computer Science, Stanford University, Stanford, California.,School of Engineering, Stanford University, Stanford, California
| | - Edward Vendrow
- Surgeons Writing About Trauma, Stanford University, Stanford, California.,Department of Computer Science, Stanford University, Stanford, California
| | - Gavin Touponse
- Surgeons Writing About Trauma, Stanford University, Stanford, California.,School of Medicine, Stanford University, Stanford, California
| | - Layla Aboukhater
- Surgeons Writing About Trauma, Stanford University, Stanford, California.,School of Medicine, Stanford University, Stanford, California
| | - Joseph D Forrester
- Department of Surgery, Stanford University, Stanford, California.,Surgeons Writing About Trauma, Stanford University, Stanford, California
| | - David A Spain
- Department of Surgery, Stanford University, Stanford, California.,Surgeons Writing About Trauma, Stanford University, Stanford, California
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Colin A, Micali G, Faure L, Cosentino Lagomarsino M, van Teeffelen S. Two different cell-cycle processes determine the timing of cell division in Escherichia coli. eLife 2021; 10:67495. [PMID: 34612203 PMCID: PMC8555983 DOI: 10.7554/elife.67495] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 10/05/2021] [Indexed: 11/13/2022] Open
Abstract
Cells must control the cell cycle to ensure that key processes are brought to completion. In Escherichia coli, it is controversial whether cell division is tied to chromosome replication or to a replication-independent inter-division process. A recent model suggests instead that both processes may limit cell division with comparable odds in single cells. Here, we tested this possibility experimentally by monitoring single-cell division and replication over multiple generations at slow growth. We then perturbed cell width, causing an increase of the time between replication termination and division. As a consequence, replication became decreasingly limiting for cell division, while correlations between birth and division and between subsequent replication-initiation events were maintained. Our experiments support the hypothesis that both chromosome replication and a replication-independent inter-division process can limit cell division: the two processes have balanced contributions in non-perturbed cells, while our width perturbations increase the odds of the replication-independent process being limiting.
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Affiliation(s)
- Alexandra Colin
- Microbial Morphogenesis and Growth Laboratory, Institut Pasteur, Paris, France
| | - Gabriele Micali
- Department of Environmental Microbiology, Dübendorf, Switzerland.,Department of Environmental Systems Science, ETH Zürich, Zürich, Switzerland
| | - Louis Faure
- Microbial Morphogenesis and Growth Laboratory, Institut Pasteur, Paris, France
| | - Marco Cosentino Lagomarsino
- IFOM, FIRC Institute of Molecular Oncology, Milan, Italy.,Physics Department, University of Milan, and INFN, Milan, Italy
| | - Sven van Teeffelen
- Microbial Morphogenesis and Growth Laboratory, Institut Pasteur, Paris, France.,Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montréal, Canada
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Palumbo D, Mori M, Prato F, Crippa S, Belfiori G, Reni M, Mushtaq J, Aleotti F, Guazzarotti G, Cao R, Steidler S, Tamburrino D, Spezi E, Del Vecchio A, Cascinu S, Falconi M, Fiorino C, De Cobelli F. Prediction of Early Distant Recurrence in Upfront Resectable Pancreatic Adenocarcinoma: A Multidisciplinary, Machine Learning-Based Approach. Cancers (Basel) 2021; 13:cancers13194938. [PMID: 34638421 PMCID: PMC8508250 DOI: 10.3390/cancers13194938] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 09/27/2021] [Accepted: 09/28/2021] [Indexed: 01/06/2023] Open
Abstract
Simple Summary If pancreatic adenocarcinoma is assessed to be technically resectable, curative surgery is still suggested as the primary treatment option; however, the recurrence rate can be very high even in this selected population. The aim of our retrospective study was to develop a preoperative model to accurately stratify upfront resectable patients according to the risk of early distant disease relapse after surgery (<12 months from index procedure). Through a machine learning-based approach, we identified one biochemical marker (serum level of CA19.9), one radiological finding (necrosis) and one radiomic feature (SurfAreaToVolumeRatio), all significantly associated with the early resurge of distant recurrence. A model composed of these three variables only allowed identification of those patients at high risk for early distant disease relapse (50% chance of developing metastases within 12 months after surgery), who would benefit from neoadjuvant chemotherapy instead of upfront surgery. Abstract Despite careful selection, the recurrence rate after upfront surgery for pancreatic adenocarcinoma can be very high. We aimed to construct and validate a model for the prediction of early distant recurrence (<12 months from index surgery) after upfront pancreaticoduodenectomy. After exclusions, 147 patients were retrospectively enrolled. Preoperative clinical and radiological (CT-based) data were systematically evaluated; moreover, 182 radiomics features (RFs) were extracted. Most significant RFs were selected using minimum redundancy, robustness against delineation uncertainty and an original machine learning bootstrap-based method. Patients were split into training (n = 94) and validation cohort (n = 53). Multivariable Cox regression analysis was first applied on the training cohort; the resulting prognostic index was then tested in the validation cohort. Clinical (serum level of CA19.9), radiological (necrosis), and radiomic (SurfAreaToVolumeRatio) features were significantly associated with the early resurge of distant recurrence. The model combining these three variables performed well in the training cohort (p = 0.0015, HR = 3.58, 95%CI = 1.98–6.71) and was then confirmed in the validation cohort (p = 0.0178, HR = 5.06, 95%CI = 1.75–14.58). The comparison of survival curves between low and high-risk patients showed a p-value <0.0001. Our model may help to better define resectability status, thus providing an actual aid for pancreatic adenocarcinoma patients’ management (upfront surgery vs. neoadjuvant chemotherapy). Independent validations are warranted.
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Affiliation(s)
- Diego Palumbo
- Department of Radiology, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy; (D.P.); (J.M.); (G.G.); (S.S.); (F.D.C.)
- School of Medicine, Vita-Salute San Raffaele University, 20132 Milan, Italy; (F.P.); (S.C.); (G.B.); (M.R.); (F.A.); (R.C.); (S.C.); (M.F.)
| | - Martina Mori
- Department of Medical Physics, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy; (M.M.); (A.D.V.)
| | - Francesco Prato
- School of Medicine, Vita-Salute San Raffaele University, 20132 Milan, Italy; (F.P.); (S.C.); (G.B.); (M.R.); (F.A.); (R.C.); (S.C.); (M.F.)
| | - Stefano Crippa
- School of Medicine, Vita-Salute San Raffaele University, 20132 Milan, Italy; (F.P.); (S.C.); (G.B.); (M.R.); (F.A.); (R.C.); (S.C.); (M.F.)
- Pancreatic Surgery Unit, Pancreas Translational and Clinical Research Center, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy;
| | - Giulio Belfiori
- School of Medicine, Vita-Salute San Raffaele University, 20132 Milan, Italy; (F.P.); (S.C.); (G.B.); (M.R.); (F.A.); (R.C.); (S.C.); (M.F.)
- Pancreatic Surgery Unit, Pancreas Translational and Clinical Research Center, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy;
| | - Michele Reni
- School of Medicine, Vita-Salute San Raffaele University, 20132 Milan, Italy; (F.P.); (S.C.); (G.B.); (M.R.); (F.A.); (R.C.); (S.C.); (M.F.)
- Department of Oncology, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Junaid Mushtaq
- Department of Radiology, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy; (D.P.); (J.M.); (G.G.); (S.S.); (F.D.C.)
- School of Medicine, Vita-Salute San Raffaele University, 20132 Milan, Italy; (F.P.); (S.C.); (G.B.); (M.R.); (F.A.); (R.C.); (S.C.); (M.F.)
| | - Francesca Aleotti
- School of Medicine, Vita-Salute San Raffaele University, 20132 Milan, Italy; (F.P.); (S.C.); (G.B.); (M.R.); (F.A.); (R.C.); (S.C.); (M.F.)
- Pancreatic Surgery Unit, Pancreas Translational and Clinical Research Center, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy;
| | - Giorgia Guazzarotti
- Department of Radiology, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy; (D.P.); (J.M.); (G.G.); (S.S.); (F.D.C.)
| | - Roberta Cao
- School of Medicine, Vita-Salute San Raffaele University, 20132 Milan, Italy; (F.P.); (S.C.); (G.B.); (M.R.); (F.A.); (R.C.); (S.C.); (M.F.)
| | - Stephanie Steidler
- Department of Radiology, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy; (D.P.); (J.M.); (G.G.); (S.S.); (F.D.C.)
| | - Domenico Tamburrino
- Pancreatic Surgery Unit, Pancreas Translational and Clinical Research Center, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy;
| | - Emiliano Spezi
- School of Engineering, Cardiff University, Cardiff CF24 3AA, UK;
| | - Antonella Del Vecchio
- Department of Medical Physics, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy; (M.M.); (A.D.V.)
| | - Stefano Cascinu
- School of Medicine, Vita-Salute San Raffaele University, 20132 Milan, Italy; (F.P.); (S.C.); (G.B.); (M.R.); (F.A.); (R.C.); (S.C.); (M.F.)
- Department of Oncology, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Massimo Falconi
- School of Medicine, Vita-Salute San Raffaele University, 20132 Milan, Italy; (F.P.); (S.C.); (G.B.); (M.R.); (F.A.); (R.C.); (S.C.); (M.F.)
- Pancreatic Surgery Unit, Pancreas Translational and Clinical Research Center, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy;
| | - Claudio Fiorino
- Department of Medical Physics, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy; (M.M.); (A.D.V.)
- Correspondence:
| | - Francesco De Cobelli
- Department of Radiology, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy; (D.P.); (J.M.); (G.G.); (S.S.); (F.D.C.)
- School of Medicine, Vita-Salute San Raffaele University, 20132 Milan, Italy; (F.P.); (S.C.); (G.B.); (M.R.); (F.A.); (R.C.); (S.C.); (M.F.)
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Belliveau NM, Chure G, Hueschen CL, Garcia HG, Kondev J, Fisher DS, Theriot JA, Phillips R. Fundamental limits on the rate of bacterial growth and their influence on proteomic composition. Cell Syst 2021; 12:924-944.e2. [PMID: 34214468 PMCID: PMC8460600 DOI: 10.1016/j.cels.2021.06.002] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 04/12/2021] [Accepted: 06/04/2021] [Indexed: 12/11/2022]
Abstract
Despite abundant measurements of bacterial growth rate, cell size, and protein content, we lack a rigorous understanding of what sets the scale of these quantities and when protein abundances should (or should not) depend on growth rate. Here, we estimate the basic requirements and physical constraints on steady-state growth by considering key processes in cellular physiology across a collection of Escherichia coli proteomic data covering ≈4,000 proteins and 36 growth rates. Our analysis suggests that cells are predominantly tuned for the task of cell doubling across a continuum of growth rates; specific processes do not limit growth rate or dictate cell size. We present a model of proteomic regulation as a function of nutrient supply that reconciles observed interdependences between protein synthesis, cell size, and growth rate and propose that a theoretical inability to parallelize ribosomal synthesis places a firm limit on the achievable growth rate. A record of this paper's transparent peer review process is included in the supplemental information.
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Affiliation(s)
- Nathan M Belliveau
- Department of Biology, Howard Hughes Medical Institute, University of Washington, Seattle, WA 98105, USA
| | - Griffin Chure
- Department of Applied Physics, California Institute of Technology, Pasadena, CA 91125, USA
| | - Christina L Hueschen
- Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA
| | - Hernan G Garcia
- Department of Molecular Cell Biology and Department of Physics, University of California Berkeley, Berkeley, CA 94720, USA
| | - Jane Kondev
- Department of Physics, Brandeis University, Waltham, MA 02453, USA
| | - Daniel S Fisher
- Department of Applied Physics, Stanford University, Stanford, CA 94305, USA
| | - Julie A Theriot
- Department of Biology, Howard Hughes Medical Institute, University of Washington, Seattle, WA 98105, USA.
| | - Rob Phillips
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; Department of Physics, California Institute of Technology, Pasadena, CA 91125, USA.
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41
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Rubin S, Agrawal A, Stegmaier J, Krief S, Felsenthal N, Svorai J, Addadi Y, Villoutreix P, Stern T, Zelzer E. Application of 3D MAPs pipeline identifies the morphological sequence chondrocytes undergo and the regulatory role of GDF5 in this process. Nat Commun 2021; 12:5363. [PMID: 34508093 PMCID: PMC8433335 DOI: 10.1038/s41467-021-25714-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 08/19/2021] [Indexed: 02/08/2023] Open
Abstract
The activity of epiphyseal growth plates, which drives long bone elongation, depends on extensive changes in chondrocyte size and shape during differentiation. Here, we develop a pipeline called 3D Morphometric Analysis for Phenotypic significance (3D MAPs), which combines light-sheet microscopy, segmentation algorithms and 3D morphometric analysis to characterize morphogenetic cellular behaviors while maintaining the spatial context of the growth plate. Using 3D MAPs, we create a 3D image database of hundreds of thousands of chondrocytes. Analysis reveals broad repertoire of morphological changes, growth strategies and cell organizations during differentiation. Moreover, identifying a reduction in Smad 1/5/9 activity together with multiple abnormalities in cell growth, shape and organization provides an explanation for the shortening of Gdf5 KO tibias. Overall, our findings provide insight into the morphological sequence that chondrocytes undergo during differentiation and highlight the ability of 3D MAPs to uncover cellular mechanisms that may regulate this process.
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Affiliation(s)
- Sarah Rubin
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Ankit Agrawal
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Johannes Stegmaier
- Institute of Imaging and Computer Vision, RWTH Aachen University, Aachen, Germany
- Institute for Automation and Applied Informatics, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Sharon Krief
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Neta Felsenthal
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Jonathan Svorai
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Yoseph Addadi
- Department of Life Science Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Paul Villoutreix
- LIS (UMR 7020), IBDM (UMR 7288), Turing Center For Living Systems, Aix-Marseille University, Marseille, France.
| | - Tomer Stern
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel.
| | - Elazar Zelzer
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel.
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Li Z, Wang Y, Liu J, Rawding P, Bu J, Hong S, Hu Q. Chemically and Biologically Engineered Bacteria-Based Delivery Systems for Emerging Diagnosis and Advanced Therapy. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2021; 33:e2102580. [PMID: 34347325 DOI: 10.1002/adma.202102580] [Citation(s) in RCA: 91] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Revised: 05/10/2021] [Indexed: 06/13/2023]
Abstract
Bacteria are one of the main groups of organisms, which dynamically and closely participate in human health and disease development. With the integration of chemical biotechnology, bacteria have been utilized as an emerging delivery system for various biomedical applications. Given the unique features of bacteria such as their intrinsic biocompatibility and motility, bacteria-based delivery systems have drawn wide interest in the diagnosis and treatment of various diseases, including cancer, infectious diseases, kidney failure, and hyperammonemia. Notably, at the interface of chemical biotechnology and bacteria, many research opportunities have been initiated, opening a promising frontier in biomedical application. Herein, the current synergy of chemical biotechnology and bacteria, the design principles for bacteria-based delivery systems, the microbial modulation, and the clinical translation are reviewed, with a special focus on the emerging advances in diagnosis and therapy.
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Affiliation(s)
- Zhaoting Li
- Pharmaceutical Sciences Division, School of Pharmacy, Wisconsin Center for NanoBioSystems, Carbone Cancer Center, School of Medicine and Public Health, University of Wisconsin, Madison (UW-Madison), Madison, Wisconsin, 53705, USA
| | - Yixin Wang
- Pharmaceutical Sciences Division, School of Pharmacy, Wisconsin Center for NanoBioSystems, Carbone Cancer Center, School of Medicine and Public Health, University of Wisconsin, Madison (UW-Madison), Madison, Wisconsin, 53705, USA
| | - Jun Liu
- Pharmaceutical Sciences Division, School of Pharmacy, Wisconsin Center for NanoBioSystems, Carbone Cancer Center, School of Medicine and Public Health, University of Wisconsin, Madison (UW-Madison), Madison, Wisconsin, 53705, USA
| | - Piper Rawding
- Pharmaceutical Sciences Division, School of Pharmacy, Wisconsin Center for NanoBioSystems, Carbone Cancer Center, School of Medicine and Public Health, University of Wisconsin, Madison (UW-Madison), Madison, Wisconsin, 53705, USA
| | - Jiyoon Bu
- Pharmaceutical Sciences Division, School of Pharmacy, Wisconsin Center for NanoBioSystems, Carbone Cancer Center, School of Medicine and Public Health, University of Wisconsin, Madison (UW-Madison), Madison, Wisconsin, 53705, USA
| | - Seungpyo Hong
- Pharmaceutical Sciences Division, School of Pharmacy, Wisconsin Center for NanoBioSystems, Carbone Cancer Center, School of Medicine and Public Health, University of Wisconsin, Madison (UW-Madison), Madison, Wisconsin, 53705, USA
| | - Quanyin Hu
- Pharmaceutical Sciences Division, School of Pharmacy, Wisconsin Center for NanoBioSystems, Carbone Cancer Center, School of Medicine and Public Health, University of Wisconsin, Madison (UW-Madison), Madison, Wisconsin, 53705, USA
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43
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Robust surface-to-mass coupling and turgor-dependent cell width determine bacterial dry-mass density. Proc Natl Acad Sci U S A 2021; 118:2021416118. [PMID: 34341116 PMCID: PMC8364103 DOI: 10.1073/pnas.2021416118] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Intracellular biomass density is an important variable for cellular physiology. It defines the crowded state of the cytoplasm and thus influences macromolecular interactions and transport. To control density during growth, bacteria must expand their cell volumes in synchrony with biomass. The regulation of volume growth and biomass density remain fundamentally not understood—in bacteria or any other organism. Using advanced microscopy, we demonstrate that cells control dry-mass density indirectly through two independent processes. First, cells expand surface area, rather than volume, in proportion with biomass growth. Second, cell width is controlled independently, with an important influence of turgor pressure. Our findings overturn a long-standing paradigm of mass-density constancy in bacteria and reveal fundamental determinants of dry-mass density and shape. During growth, cells must expand their cell volumes in coordination with biomass to control the level of cytoplasmic macromolecular crowding. Dry-mass density, the average ratio of dry mass to volume, is roughly constant between different nutrient conditions in bacteria, but it remains unknown whether cells maintain dry-mass density constant at the single-cell level and during nonsteady conditions. Furthermore, the regulation of dry-mass density is fundamentally not understood in any organism. Using quantitative phase microscopy and an advanced image-analysis pipeline, we measured absolute single-cell mass and shape of the model organisms Escherichia coli and Caulobacter crescentus with improved precision and accuracy. We found that cells control dry-mass density indirectly by expanding their surface, rather than volume, in direct proportion to biomass growth—according to an empirical surface growth law. At the same time, cell width is controlled independently. Therefore, cellular dry-mass density varies systematically with cell shape, both during the cell cycle or after nutrient shifts, while the surface-to-mass ratio remains nearly constant on the generation time scale. Transient deviations from constancy during nutrient shifts can be reconciled with turgor-pressure variations and the resulting elastic changes in surface area. Finally, we find that plastic changes of cell width after nutrient shifts are likely driven by turgor variations, demonstrating an important regulatory role of mechanical forces for width regulation. In conclusion, turgor-dependent cell width and a slowly varying surface-to-mass coupling constant are the independent variables that determine dry-mass density.
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Lim JH, Lee CW, Bong CW, Kudo I. The impact of eutrophication towards selected bacterial process rates in tropical coastal waters. MARINE POLLUTION BULLETIN 2021; 169:112524. [PMID: 34049069 DOI: 10.1016/j.marpolbul.2021.112524] [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: 01/28/2021] [Revised: 04/04/2021] [Accepted: 04/25/2021] [Indexed: 06/12/2023]
Abstract
The dissolved organic nutrient conditions and bacterial process rates at two tropical coastal sites in Peninsular Malaysia (Port Klang and Port Dickson) were initially studied in 2004-2005 period and later revisited in 2010-2011. We observed that dissolved organic nitrogen (DON) increased about two- and ten-fold at Port Klang and Port Dickson, respectively and resulted in a significant change in DOC:DON ratio (t ≥ 2.077, p < 0.05). Among the bacterial processes measured, bacterial respiration (BR) was lower in the 2010-2011 period at both stations (t ≥ 3.390, p < 0.01). BR also correlated to the DOC:DON ratio (R2 ≥ 0.259, p < 0.01). The increase in substrate quality enabled the bacteria to respire less in the dissolved organic matter degradation. As a result, the average bacterial growth efficiency increased slightly in the 2010-2011 period.
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Affiliation(s)
- Joon Hai Lim
- Laboratory of Microbial Ecology, Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia; Institute of Ocean and Earth Sciences, University of Malaya, 50603 Kuala Lumpur, Malaysia; Institute for Advanced Studies, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Choon Weng Lee
- Laboratory of Microbial Ecology, Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia; Institute of Ocean and Earth Sciences, University of Malaya, 50603 Kuala Lumpur, Malaysia.
| | - Chui Wei Bong
- Laboratory of Microbial Ecology, Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia; Institute of Ocean and Earth Sciences, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Isao Kudo
- Graduate School of Fisheries Sciences, Hokkaido University, Sapporo, Japan
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YAP1 nuclear efflux and transcriptional reprograming follow membrane diminution upon VSV-G-induced cell fusion. Nat Commun 2021; 12:4502. [PMID: 34301937 PMCID: PMC8302681 DOI: 10.1038/s41467-021-24708-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 06/24/2021] [Indexed: 02/07/2023] Open
Abstract
Cells in many tissues, such as bone, muscle, and placenta, fuse into syncytia to acquire new functions and transcriptional programs. While it is known that fused cells are specialized, it is unclear whether cell-fusion itself contributes to programmatic-changes that generate the new cellular state. Here, we address this by employing a fusogen-mediated, cell-fusion system to create syncytia from undifferentiated cells. RNA-Seq analysis reveals VSV-G-induced cell fusion precedes transcriptional changes. To gain mechanistic insights, we measure the plasma membrane surface area after cell-fusion and observe it diminishes through increases in endocytosis. Consequently, glucose transporters internalize, and cytoplasmic glucose and ATP transiently decrease. This reduced energetic state activates AMPK, which inhibits YAP1, causing transcriptional-reprogramming and cell-cycle arrest. Impairing either endocytosis or AMPK activity prevents YAP1 inhibition and cell-cycle arrest after fusion. Together, these data demonstrate plasma membrane diminishment upon cell-fusion causes transient nutrient stress that may promote transcriptional-reprogramming independent from extrinsic cues.
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46
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Phillips R. Schrödinger's What Is Life? at 75. Cell Syst 2021; 12:465-476. [PMID: 34139159 DOI: 10.1016/j.cels.2021.05.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 02/09/2021] [Accepted: 05/17/2021] [Indexed: 11/15/2022]
Abstract
2019 marked the 75th anniversary of the publication of Erwin Schrödinger's What Is Life?, a short book described by Roger Penrose in his preface to a reprint of this classic as "among the most influential scientific writings of the 20th century." In this article, I review the long argument made by Schrödinger as he mused on how the laws of physics could help us understand "the events in space and time which take place within the spatial boundary of a living organism." Though Schrödinger's book is often hailed for its influence on some of the titans who founded molecular biology, this article takes a different tack. Instead of exploring the way the book touched biologists such as James Watson and Francis Crick, as well as its critical reception by others such as Linus Pauling and Max Perutz, I argue that Schrödinger's classic is a timeless manifesto, rather than a dated historical curiosity. What Is Life? is full of timely outlooks and approaches to understanding the mysterious living world that includes and surrounds us and can instead be viewed as a call to arms to tackle the great unanswered challenges in the study of living matter that remain for 21st century science.
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Affiliation(s)
- Rob Phillips
- Division of Biology and Biological Engineering and Department of Physics, California Institute of Technology, Pasadena, California, USA.
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47
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Wang L, Li P, Zhang Q, Wu WM, Luo J, Hou D. Modeling the Conditional Fragmentation-Induced Microplastic Distribution. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:6012-6021. [PMID: 33840192 DOI: 10.1021/acs.est.1c01042] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Microplastics (MPs) are drawing increasing attention from the international community due to their potential threats to the ecosystem and human health. Although their occurrence and spatial distribution have been extensively studied in recent years, the relationship between their abundance and sizes remains unclear. Moreover, the underlying mechanisms dominating their size distribution have rarely been explored. In the present study, we developed a novel conditional fragmentation model to describe MP size distribution in the soil environment. It is proposed that the distribution of MPs is not a coincidence but controlled by conditional aging. The applicability of this model was tested using data collected from different land use settings in Beijing, China. A distinct downsizing phenomenon from fibers, films, and fragments to granules is observed. Undisturbed land use types accumulated larger sized MPs with higher stability, while human interference accelerated the fragmentation of MPs. Both morphological analysis and time-of-flight secondary ion mass spectroscopy (TOF-SIMS) observations provided direct evidence for the conditional fragmentation process. Furthermore, the model has proven to be suitable for describing the size distribution of MPs from various sources (including atmospheric deposition, transportation, and agriculture) and aging processes (such as mechanical abrasion, chemical oxidation, and photochemical transformation). It is proposed that this model can be used for various purposes in MP-related studies, especially source identification, transport modeling, and risk assessment.
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Affiliation(s)
- Liuwei Wang
- School of Environment, Tsinghua University, Beijing 100084, China
| | - Pengfei Li
- School of Environment, Tsinghua University, Beijing 100084, China
| | - Qi Zhang
- School of Environment, Tsinghua University, Beijing 100084, China
| | - Wei-Min Wu
- Department of Civil and Environmental Engineering, William & Cloy Codiga Resource Recovery Center, Center for Sustainable Development & Global Competitiveness, Stanford University, Stanford, California 94305-4020, United States
| | - Jian Luo
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0355, United States
| | - Deyi Hou
- School of Environment, Tsinghua University, Beijing 100084, China
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48
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Threshold accumulation of a constitutive protein explains E. coli cell-division behavior in nutrient upshifts. Proc Natl Acad Sci U S A 2021; 118:2016391118. [PMID: 33931503 DOI: 10.1073/pnas.2016391118] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Despite a boost of recent progress in dynamic single-cell measurements and analyses in Escherichia coli, we still lack a mechanistic understanding of the determinants of the decision to divide. Specifically, the debate is open regarding the processes linking growth and chromosome replication to division and on the molecular origin of the observed "adder correlations," whereby cells divide, adding roughly a constant volume independent of their initial volume. In order to gain insight into these questions, we interrogate dynamic size-growth behavior of single cells across nutrient upshifts with a high-precision microfluidic device. We find that the division rate changes quickly after nutrients change, much before growth rate goes to a steady state, and in a way that adder correlations are robustly conserved. Comparison of these data to simple mathematical models falsifies proposed mechanisms, where replication-segregation or septum completions are the limiting step for cell division. Instead, we show that the accumulation of a putative constitutively expressed "P-sector divisor" protein explains the behavior during the shift.
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Strain-specific interaction of Fructilactobacillus sanfranciscensis with yeasts in the sourdough fermentation. Eur Food Res Technol 2021. [DOI: 10.1007/s00217-021-03722-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
AbstractFructilactobacillus (F.) sanfranciscensis is a key bacterium in traditional (type 1) sourdough fermentations. It typically occurs in combination with the sourdough yeast Kazachstania (K.) humilis or the generalist Saccharomyces (S.) cerevisiae. Previous studies revealed intra-species diversity in competitiveness or dominance in sourdoughs of F. sanfranciscensis, as well as preferences for a life with or without a specific yeast. In this study representative, differently behaving strains were studied in media with different sugars and electron acceptors, and in rye sourdough fermentations in the presence and absence of K. humilis or S. cerevisiae. Strain-specific differences were observed in sugar and organic acids spectra in media, and in sourdoughs with F. sanfranciscensis strains in combination with K. humilis or S. cerevisiae. F. sanfranciscensis TMW 1.1150 proved dominant in the presence and absence of any yeast because it most effectively used maltose. Its maltose fermentation was unaffected by electron acceptors. F. sanfranciscensis TMW 1.2138 was the weakest maltose fermenter and incapable of glucose fermentation, and evidently not competitive against the other strains. F. sanfranciscensis TMW 1.392 was the most versatile strain regarding the utilization of different carbohydrates and its ability to exploit electron acceptors like fructose and oxygen. In sourdoughs without yeasts, it outcompeted other strains. The metabolism of F. sanfranciscensis TMW 1.907 was stimulated in combination with S. cerevisiae. In competitive trials, it was assertive only with S. cerevisiae. The intra-species differences in carbohydrate metabolism can widely explain the differences in their behavior in sourdough fermentation. Interaction between F. sanfranciscensis and the yeasts was strain specific and supposedly commensal with K. humilis and rather competitive with S. cerevisiae.
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50
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Grant NA, Abdel Magid A, Franklin J, Dufour Y, Lenski RE. Changes in Cell Size and Shape during 50,000 Generations of Experimental Evolution with Escherichia coli. J Bacteriol 2021; 203:e00469-20. [PMID: 33649147 PMCID: PMC8088598 DOI: 10.1128/jb.00469-20] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 02/18/2021] [Indexed: 02/07/2023] Open
Abstract
Bacteria adopt a wide variety of sizes and shapes, with many species exhibiting stereotypical morphologies. How morphology changes, and over what timescales, is less clear. Previous work examining cell morphology in an experiment with Escherichia coli showed that populations evolved larger cells and, in some cases, cells that were less rod-like. That experiment has now run for over two more decades. Meanwhile, genome sequence data are available for these populations, and new computational methods enable high-throughput microscopic analyses. In this study, we measured stationary-phase cell volumes for the ancestor and 12 populations at 2,000, 10,000, and 50,000 generations, including measurements during exponential growth at the last time point. We measured the distribution of cell volumes for each sample using a Coulter counter and microscopy, the latter of which also provided data on cell shape. Our data confirm the trend toward larger cells while also revealing substantial variation in size and shape across replicate populations. Most populations first evolved wider cells but later reverted to the ancestral length-to-width ratio. All but one population evolved mutations in rod shape maintenance genes. We also observed many ghost-like cells in the only population that evolved the novel ability to grow on citrate, supporting the hypothesis that this lineage struggles with maintaining balanced growth. Lastly, we show that cell size and fitness remain correlated across 50,000 generations. Our results suggest that larger cells are beneficial in the experimental environment, while the reversion toward ancestral length-to-width ratios suggests partial compensation for the less favorable surface area-to-volume ratios of the evolved cells.IMPORTANCE Bacteria exhibit great morphological diversity, yet we have only a limited understanding of how their cell sizes and shapes evolve and of how these features affect organismal fitness. This knowledge gap reflects, in part, the paucity of the fossil record for bacteria. In this study, we revived and analyzed samples extending over 50,000 generations from 12 populations of experimentally evolving Escherichia coli to investigate the relation between cell size, shape, and fitness. Using this "frozen fossil record," we show that all 12 populations evolved larger cells concomitant with increased fitness, with substantial heterogeneity in cell size and shape across the replicate lines. Our work demonstrates that cell morphology can readily evolve and diversify, even among populations living in identical environments.
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Affiliation(s)
- Nkrumah A Grant
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
- BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, Michigan, USA
- Ecology, Evolutionary Biology, and Behavior Program, Michigan State University, East Lansing, Michigan, USA
| | - Ali Abdel Magid
- BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, Michigan, USA
| | - Joshua Franklin
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
- BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, Michigan, USA
| | - Yann Dufour
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
- BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, Michigan, USA
| | - Richard E Lenski
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
- BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, Michigan, USA
- Ecology, Evolutionary Biology, and Behavior Program, Michigan State University, East Lansing, Michigan, USA
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