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Gui R, Jin H. Organic fluorophores-based molecular probes with dual-fluorescence ratiometric responses to in-vitro/in-vivo pH for biosensing, bioimaging and biotherapeutics applications. Talanta 2024; 275:126171. [PMID: 38703479 DOI: 10.1016/j.talanta.2024.126171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 04/19/2024] [Accepted: 04/25/2024] [Indexed: 05/06/2024]
Abstract
In recent years, organic fluorophores-based molecular probes with dual-fluorescence ratiometric responses to in-vitro/in-vivo pH (DFR-MPs-pH) have been attracting much interest in fundamental application research fields. More and more scientific publications have reported the exploration of various DFR-MPs-pH systems that have unique dual-fluorescence ratiometry as the signal output, in-built and signal self-calibration functions to improve precise detection of targets. DFR-MPs-pH systems possess high-performance applications in biosensing, bioimaging and biomedicine fields. This review has comprehensively summarized recent advances of DFR-MPs-pH for the first time. First of all, the compositions and types of DFR-MPs-pH are introduced by summarizing different organic fluorophores-based molecule systems. Then, construction strategies are analyzed based on specific components, structures, properties and functions of DFR-MPs-pH. Afterward, biosensing and bioimaging applications are discussed in detail, primarily referring to pH sensing and imaging detection at the levels of living cells and small animals. Finally, biomedicine applications are fully summarized, majorly involving bio-toxicity evaluation, bio-distribution, biomedical diagnosis and therapeutics. Meanwhile, the current status, challenges and perspectives are rationally commented after detailed discussions of representative and state-of-the-art studies. Overall, this present review is comprehensive, in-time and in-depth, and can facilitate the following further exploration of new and versatile DFR-MPs-pH systems toward rational design, facile preparation, superior properties, adjustable functions and highly efficient applications in promising fields.
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Affiliation(s)
- Rijun Gui
- College of Chemistry and Chemical Engineering, Intellectual Property Research Institute, Qingdao University, Shandong, 266071, PR China.
| | - Hui Jin
- College of Chemistry and Chemical Engineering, Intellectual Property Research Institute, Qingdao University, Shandong, 266071, PR China
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2
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Belashov AV, Zhikhoreva AA, Salova AV, Belyaeva TN, Litvinov IK, Kornilova ES, Semenova IV, Vasyutinskii OS. Automatic segmentation of lysosomes and analysis of intracellular pH with Radachlorin photosensitizer and FLIM. Biochem Biophys Res Commun 2024; 710:149835. [PMID: 38574457 DOI: 10.1016/j.bbrc.2024.149835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 03/17/2024] [Accepted: 03/25/2024] [Indexed: 04/06/2024]
Abstract
We report application of the fluorescence lifetime imaging microscopy (FLIM) for analysis of distributions of intracellular acidity using a chlorin-e6 based photosensitizer Radachlorin. An almost two-fold increase of the photosensitizer fluorescence lifetime in alkaline microenvironments as compared to acidic ones allowed for clear distinguishing between acidic and alkaline intracellular structures. Clusterization of a phasor plot calculated from fits of the FLIM raw data by two Gaussian distributions provided accurate automatic segmentation of lysosomes featuring acidic contents. The approach was validated in colocalization experiments with LysoTracker fluorescence in living cells of four established lines. The dependence of photosensitizer fluorescence lifetime on microenvironment acidity allowed for estimation of pH inside the cells, except for the nuclei, where photosensitizer does not penetrate. The developed method is promising for combined application of the photosensitizer for both photodynamic treatment and diagnostics.
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Affiliation(s)
- A V Belashov
- Ioffe Institute, Russian Academy of Sciences, 26, Polytekhnicheskaya, St.Petersburg, 194021, Russia
| | - A A Zhikhoreva
- Ioffe Institute, Russian Academy of Sciences, 26, Polytekhnicheskaya, St.Petersburg, 194021, Russia
| | - A V Salova
- Institute of Cytology, Russian Academy of Sciences, Tikhoretsky Pr., 4, St. Petersburg, 194064, Russia
| | - T N Belyaeva
- Institute of Cytology, Russian Academy of Sciences, Tikhoretsky Pr., 4, St. Petersburg, 194064, Russia
| | - I K Litvinov
- Institute of Cytology, Russian Academy of Sciences, Tikhoretsky Pr., 4, St. Petersburg, 194064, Russia
| | - E S Kornilova
- Institute of Cytology, Russian Academy of Sciences, Tikhoretsky Pr., 4, St. Petersburg, 194064, Russia
| | - I V Semenova
- Ioffe Institute, Russian Academy of Sciences, 26, Polytekhnicheskaya, St.Petersburg, 194021, Russia.
| | - O S Vasyutinskii
- Ioffe Institute, Russian Academy of Sciences, 26, Polytekhnicheskaya, St.Petersburg, 194021, Russia
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3
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Gao Y, Yin B, Liu X, Wu S. Difunctional Microelectrode Arrays for Single-Cell Electrical Stimulation and pH Detection. Anal Chem 2024; 96:2087-2093. [PMID: 38275169 DOI: 10.1021/acs.analchem.3c04766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2024]
Abstract
Due to its direct effect on biomolecules and cells, electrical stimulation (ES) is now widely used to regulate cell proliferation, differentiation, and neurostimulation and is even used in the clinic for pain relief, treatment of nerve damage, and muscle rehabilitation. Conventional ES is mostly studied on cell populations, but the heterogeneity of cancer cells results in the inability to access the response of individual cells to ES. Therefore, detecting the extracellular pH change (ΔpHe) after ES at the single-cell level is important for the application of ES in tumor therapy. In this study, cellular ΔpHe after periodic impulse electrostimulation (IES) was monitored in situ by using a polyaniline (PANI)-modified gold microelectrode array. The PANI sensor had excellent sensitivity (53.68 mV/pH) and linear correlation coefficient (R2 = 0.999) over the pH range of 5.55-7.41. The cells showed different degrees of ΔpHe after the IES with different intervals and stimulation potential. A shorter pulse interval and a higher stimulation potential could effectively enhance stimulation and increase cellular ΔpHe. At 0.5 V potential stimulation, the cellular ΔpHe increased with decreasing pulse interval. However, if the pulse interval was long enough, even at a higher potential of 0.7 V, there was no significant additional ΔpHe due to the insufficient stimulus strength. Based on the above conclusions, the prepared PANI microelectrode arrays (MEAs) were capable of stimulating and detecting single cells, which contributed to the deeper application of ES in tumor therapy.
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Affiliation(s)
- Yuan Gao
- School of Chemistry, Dalian University of Technology, Dalian 116023, P. R. China
| | - Bing Yin
- School of Chemistry, Dalian University of Technology, Dalian 116023, P. R. China
| | - Xiaobo Liu
- School of Chemistry, Dalian University of Technology, Dalian 116023, P. R. China
| | - Shuo Wu
- School of Chemistry, Dalian University of Technology, Dalian 116023, P. R. China
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4
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DeBenedictis EA, Chory EJ, Gretton DW, Wang B, Golas S, Esvelt KM. Systematic molecular evolution enables robust biomolecule discovery. Nat Methods 2022; 19:55-64. [PMID: 34969982 DOI: 10.1038/s41592-021-01348-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 11/09/2021] [Indexed: 11/09/2022]
Abstract
Evolution occurs when selective pressures from the environment shape inherited variation over time. Within the laboratory, evolution is commonly used to engineer proteins and RNA, but experimental constraints have limited the ability to reproducibly and reliably explore factors such as population diversity, the timing of environmental changes and chance on outcomes. We developed a robotic system termed phage- and robotics-assisted near-continuous evolution (PRANCE) to comprehensively explore biomolecular evolution by performing phage-assisted continuous evolution in high-throughput. PRANCE implements an automated feedback control system that adjusts the stringency of selection in response to real-time measurements of each molecular activity. In evolving three distinct types of biomolecule, we find that evolution is reproducibly altered by both random chance and the historical pattern of environmental changes. This work improves the reliability of protein engineering and enables the systematic analysis of the historical, environmental and random factors governing biomolecular evolution.
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Affiliation(s)
- Erika A DeBenedictis
- Media Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA. .,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Emma J Chory
- Media Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA.,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.,Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Dana W Gretton
- Media Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Brian Wang
- Media Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Stefan Golas
- Media Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Kevin M Esvelt
- Media Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA.
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5
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Choi D, Choi M, Jeong H, Heo J, Kim T, Park S, Jin Y, Lee S, Hong J. Co-existing "spear-and-shield" air filter: Anchoring proteinaceous pathogen and self-sterilized nanocoating for combating viral pandemic. CHEMICAL ENGINEERING JOURNAL (LAUSANNE, SWITZERLAND : 1996) 2021; 426:130763. [PMID: 34131388 PMCID: PMC8192840 DOI: 10.1016/j.cej.2021.130763] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 05/23/2021] [Accepted: 06/05/2021] [Indexed: 06/12/2023]
Abstract
Infectious pollutants bioaerosols can threaten human public health. In particular, the indoor environment provides a unique exposure situation to induce infection through airborne transmission like SARS-CoV-2. To prevent the infection from spreading, personal protective equipment or indoor air purification is necessary. However, it has been discovered that the conventional filter can become contaminated by pathogen-containing aerosols, meaning that advanced filtering and self-sterilization systems are required. Here, we fabricate a multilayered nanocoating around the fabric using laponite (LAP) with Cu2+ ions (LAP-Cu2+ nanocoating) two contradictory functions in one system: trapping proteinaceous pathogens and antibacterial effect. Due to the strong LAP-protein interaction, albumin and spike protein (S-protein) are trapped into the fabric when proteins are sprayed using a nebulizer. The protein-blocking performance of the nanocoated fabric is 9.55-fold higher than bare fabric. These trapping capacities are retained after rinsing and repeated adsorption cycles, showing reproducibility for air filtration. Even though the protein-binding occurred, the LAP-Cu2+ fabric indicates antibacterial effect. LAP-Cu2+ fabric has an equivalent air and water transmittance rate to that of bare fabric with a stability under physiological environment. Therefore, given its excellent "Spear-and-shield" functions, the proposed LAP-Cu2+ fabric shows great potential for use in filter and masks during the viral pandemic.
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Affiliation(s)
- Daheui Choi
- Department of Chemical and Biomolecular Engineering, Yonsei University, Seoul 03722, Republic of Korea
| | - Moonhyun Choi
- Department of Chemical and Biomolecular Engineering, Yonsei University, Seoul 03722, Republic of Korea
| | - Hyejoong Jeong
- Department of Chemical and Biomolecular Engineering, Yonsei University, Seoul 03722, Republic of Korea
| | - Jiwoong Heo
- Department of Chemical and Biomolecular Engineering, Yonsei University, Seoul 03722, Republic of Korea
| | - Taihyun Kim
- Department of Chemical and Biomolecular Engineering, Yonsei University, Seoul 03722, Republic of Korea
| | - Sohyeon Park
- Department of Chemical and Biomolecular Engineering, Yonsei University, Seoul 03722, Republic of Korea
| | - Youngho Jin
- Agency for Defense Development, Daejeon 34186, Republic of Korea
| | - Sangmin Lee
- School of Mechanical Engineering, Chung-ang University, Seoul 06974, Republic of Korea
| | - Jinkee Hong
- Department of Chemical and Biomolecular Engineering, Yonsei University, Seoul 03722, Republic of Korea
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6
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Won S, Ha MG, Nguyen DD, Kang HY. Biological selenite removal and recovery of selenium nanoparticles by haloalkaliphilic bacteria isolated from the Nakdong River. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 280:117001. [PMID: 33799130 DOI: 10.1016/j.envpol.2021.117001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Revised: 02/09/2021] [Accepted: 03/18/2021] [Indexed: 06/12/2023]
Abstract
Microbial selenite reduction has increasingly attracted attention from the scientific community because it allows the separation of toxic Se from waste sources with the concurrent recovery of Se nanoparticles, a multifunctional material in nanotechnology industries. In this study, four selenite-reducing bacteria, isolated from a river water sample, were found to reduce selenite by > 85% within 3 d of incubation, at ambient temperature. Among them, strain NDSe-7, belonging to genus Lysinibacillus, can reduce selenite and produce Se nanospheres in alkaline conditions, up to pH 10.0, and in salinity of up to 7.0%. This strain can reduce 80 mg/L of selenite to elemental Se within 24 h at pH 6.0-8.0, at a temperature of 30-40 °C, and salinity of 0.1-3.5%. Strain NDSe-7 exhibited potential for use in Se removal and recovery from industrial saline wastewater with high alkalinity. This study indicates that extremophilic microorganisms for environmental remediation can be found in a conventional environment.
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Affiliation(s)
- Sangmin Won
- Department of Microbiology, Pusan National University, Busan, 46241, Republic of Korea.
| | - Myung-Gyu Ha
- Korea Basic Science Institute, Busan Center, Busan, 46742, Republic of Korea
| | - Dinh Duc Nguyen
- Department of Environmental Energy Engineering, Kyonggi University, Suwon, 16227, Republic of Korea; Faculty of Environmental and Food Engineering, Nguyen Tat Thanh University, 300A Nguyen Tat Thanh, District 4, Ho Chi Minh City, 755414, Viet Nam
| | - Ho Young Kang
- Department of Microbiology, Pusan National University, Busan, 46241, Republic of Korea.
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7
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Nussbaumer-Pröll AK, Eberl S, Reiter B, Stimpfl T, Dorn C, Zeitlinger M. Low pH reduces the activity of ceftolozane/tazobactam in human urine, but confirms current breakpoints for urinary tract infections. J Antimicrob Chemother 2021; 75:593-599. [PMID: 31794023 DOI: 10.1093/jac/dkz488] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 10/22/2019] [Accepted: 10/24/2019] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Acidic pH has been shown to impact the antibiotic activity of non-β-lactams in urine. OBJECTIVES To investigate the in vitro activity of ceftolozane/tazobactam compared with meropenem at different pH settings in urine. METHODS We determined the MICs for 30 clinical isolates of Escherichia coli, 25 clinical isolates of Klebsiella pneumoniae and 24 clinical isolates of Proteus mirabilis in pooled human urine and standard growth medium at pH 5 and 7. Time-kill curves were produced for one representative clinical isolate of tested bacterial strains in urine at pH 5, 6 and 7 for both antibiotics at concentrations above and below the MIC. HPLC analysis of the stability of ceftolozane/tazobactam and meropenem was performed at different pH values. RESULTS The median MICs of both antibiotics were up to 8-fold higher at pH 5 than at pH 7. Bacterial growth of E. coli was not impacted by pH, while for K. pneumoniae and P. mirabilis low pH slightly reduced growth. Compared with pH 7, pH 5 resulted in a significant decrease in antibiotic activity with a delta of up to 3 log10 bacterial counts after 24 h. Impact of acidic pH was lowest for P. mirabilis; however, this strain metabolically increased the pH during experiments. Stability was not impacted by low pH. CONCLUSIONS Acidic pH had a significant negative impact on the activity of ceftolozane/tazobactam and meropenem in urine. Considering concentrations achieved in urine, our results confirm existing breakpoints and do not advocate increasing ceftolozane/tazobactam breakpoints for urinary tract infections.
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Affiliation(s)
| | - Sabine Eberl
- Department of Clinical Pharmacology, Medical University of Vienna, Vienna, Austria
| | - Birgit Reiter
- Clinical Department of Medical and Chemical Laboratory Diagnostics, Medical University of Vienna, Vienna, Austria
| | - Thomas Stimpfl
- Clinical Department of Medical and Chemical Laboratory Diagnostics, Medical University of Vienna, Vienna, Austria
| | - Christoph Dorn
- Institute of Pharmacy, University of Regensburg, Regensburg, Germany
| | - Markus Zeitlinger
- Department of Clinical Pharmacology, Medical University of Vienna, Vienna, Austria
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8
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Chory EJ, Gretton DW, DeBenedictis EA, Esvelt KM. Enabling high-throughput biology with flexible open-source automation. Mol Syst Biol 2021; 17:e9942. [PMID: 33764680 PMCID: PMC7993322 DOI: 10.15252/msb.20209942] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Revised: 02/03/2021] [Accepted: 02/05/2021] [Indexed: 12/19/2022] Open
Abstract
Our understanding of complex living systems is limited by our capacity to perform experiments in high throughput. While robotic systems have automated many traditional hand-pipetting protocols, software limitations have precluded more advanced maneuvers required to manipulate, maintain, and monitor hundreds of experiments in parallel. Here, we present Pyhamilton, an open-source Python platform that can execute complex pipetting patterns required for custom high-throughput experiments such as the simulation of metapopulation dynamics. With an integrated plate reader, we maintain nearly 500 remotely monitored bacterial cultures in log-phase growth for days without user intervention by taking regular density measurements to adjust the robotic method in real-time. Using these capabilities, we systematically optimize bioreactor protein production by monitoring the fluorescent protein expression and growth rates of a hundred different continuous culture conditions in triplicate to comprehensively sample the carbon, nitrogen, and phosphorus fitness landscape. Our results demonstrate that flexible software can empower existing hardware to enable new types and scales of experiments, empowering areas from biomanufacturing to fundamental biology.
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Affiliation(s)
- Emma J Chory
- Media LaboratoryMassachusetts Institute of TechnologyCambridgeMAUSA
- Institute for Medical Engineering and ScienceMassachusetts Institute of TechnologyCambridgeMAUSA
- Broad Institute of MIT and HarvardCambridgeMAUSA
| | - Dana W Gretton
- Media LaboratoryMassachusetts Institute of TechnologyCambridgeMAUSA
| | - Erika A DeBenedictis
- Media LaboratoryMassachusetts Institute of TechnologyCambridgeMAUSA
- Department of Biological EngineeringMassachusetts Institute of TechnologyCambridgeMAUSA
| | - Kevin M Esvelt
- Media LaboratoryMassachusetts Institute of TechnologyCambridgeMAUSA
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9
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Highlighting Curcumin-Induced Crosstalk between Autophagy and Apoptosis as Supported by Its Specific Subcellular Localization. Cells 2020; 9:cells9020361. [PMID: 32033136 PMCID: PMC7072416 DOI: 10.3390/cells9020361] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 01/08/2020] [Accepted: 01/15/2020] [Indexed: 12/31/2022] Open
Abstract
Curcumin, a major active component of turmeric (Curcuma longa, L.), is known to have various effects on both healthy and cancerous tissues. In vitro studies suggest that curcumin inhibits cancer cell growth by activating apoptosis, but the mechanism underlying the anticancer effect of curcumin is still unclear. Since there is a recent consensus about endoplasmic reticulum (ER) stress being involved in the cytotoxicity of natural compounds, we have investigated using Image flow cytometry the mechanistic aspects of curcumin's destabilization of the ER, but also the status of the lysosomal compartment. Curcumin induces ER stress, thereby causing an unfolded protein response and calcium release, which destabilizes the mitochondrial compartment and induce apoptosis. These events are also associated with secondary lysosomal membrane permeabilization that occurs later together with an activation of caspase-8, mediated by cathepsins and calpains that ended in the disruption of mitochondrial homeostasis. These two pathways of different intensities and momentum converge towards an amplification of cell death. In the present study, curcumin-induced autophagy failed to rescue all cells that underwent type II cell death following initial autophagic processes. However, a small number of cells were rescued (successful autophagy) to give rise to a novel proliferation phase.
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10
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Bonanno A, Pérez-Herráez I, Zaballos-García E, Pérez-Prieto J. Gold nanoclusters for ratiometric sensing of pH in extremely acidic media. Chem Commun (Camb) 2020; 56:587-590. [DOI: 10.1039/c9cc08539d] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
AuNCs capped with β-nicotinamide adenine dinucleotide phosphate exhibit an outstanding performance as ratiometric, fluorescent pH sensors in extremely acid media (0.6–2.7) and in the 7.0–9.2 pH range; the nanocluster itself is the fluorophore.
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Affiliation(s)
- Adele Bonanno
- Departamento de Química Orgánica
- Universidad de Valencia
- Av. Vicent Andres Estelles s/n
- Burjassot
- Spain
| | - Irene Pérez-Herráez
- Instituto de Ciencia Molecular (ICMol)
- Universidad de Valencia
- Catedrático José Beltrán 2
- Valencia
- Spain
| | - Elena Zaballos-García
- Departamento de Química Orgánica
- Universidad de Valencia
- Av. Vicent Andres Estelles s/n
- Burjassot
- Spain
| | - Julia Pérez-Prieto
- Instituto de Ciencia Molecular (ICMol)
- Universidad de Valencia
- Catedrático José Beltrán 2
- Valencia
- Spain
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11
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Alafeef M, Dighe K, Pan D. Label-Free Pathogen Detection Based on Yttrium-Doped Carbon Nanoparticles up to Single-Cell Resolution. ACS APPLIED MATERIALS & INTERFACES 2019; 11:42943-42955. [PMID: 31647216 DOI: 10.1021/acsami.9b14110] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
The capability to detect bacteria at a low cell density is critical to prevent the delay in therapeutic intervention and to avoid the emergence of antibiotic-resistant species. Till date, significant advancement has been made to develop a sensing platform for rapid and reliable bacterial detection. However, critical requirements, that is, limit of detection, fast time of response, ultrasensitivity with high reproducibility, and the ability to distinguish between bacterial strains are yet to be met within a single sensing platform. In this contribution, we present a novel label-free sensor based on pH-sensitive fluorescent yttrium-doped carbon nanoparticles (YCNPs) embedded in agarose that can rapidly and accurately detect and discriminate pathogens in real time. The developed sensor matrix presented pH-triggered aggregation-induced emission quenching of YCNPs in a wide pH range. When the pH decreased from 10.0 to 4.0, the fluorescence of the matrix decreased linearly (R2 = 0.9229). The sensor 's high sensitivity in a physiologically relevant pH range enables the monitoring of the presence of live pathogens to single-cell resolution. In addition, the 3D matrix sensor showed low cytotoxicity and long stability (>30 days). Besides, the YCNP platform is stable for several hours (5 h) in a complex medium and does not alter the bacterial activities, allowing real-time monitoring of bacterial growth with a small sample volume (100 μL) and rapid response time (25 min). Furthermore, using machine learning-assisted tools, different bacterial strains with various cell densities were discriminated with an accuracy of almost 100%. Moreover, blends of pathogens and a real-world sample can also be identified accurately, thus enabling the sensor to provide fast and reliable pathogen information for clinical decisions and allowing continuous monitoring of infectious disease trends.
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Affiliation(s)
- Maha Alafeef
- Mills Breast Cancer Institute , Carle Foundation Hospital , Urbana , Illinois 61801 , United States
- Biomedical Engineering Department , Jordan University of Science and Technology , Irbid 22110 , Jordan
| | - Ketan Dighe
- Mills Breast Cancer Institute , Carle Foundation Hospital , Urbana , Illinois 61801 , United States
| | - Dipanjan Pan
- Mills Breast Cancer Institute , Carle Foundation Hospital , Urbana , Illinois 61801 , United States
- Carle Illinois College of Medicine , 807 South Wright Street , Urbana , Illinois 61801 , United States
- Department of Diagnostic Radiology and Nuclear Medicine and Department of Chemical, Biochemical and Environmental Engineering , University of Maryland Baltimore and University of Baltimore County , 1000 Hilltop Circle , Baltimore , Maryland 21250 , United States
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12
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Nguyen VK, Choi W, Ha Y, Gu Y, Lee C, Park J, Jang G, Shin C, Cho S. Microbial tellurite reduction and production of elemental tellurium nanoparticles by novel bacteria isolated from wastewater. J IND ENG CHEM 2019. [DOI: 10.1016/j.jiec.2019.06.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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13
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Pan T, Yang C, Li J, Jiang J, Wen J, Wang Z, Zhong K, Tian Y, Chen M. High-throughput extracellular pH monitoring and antibiotics screening by polymeric fluorescent sensor with LCST property. Methods 2019; 168:51-61. [PMID: 31051251 DOI: 10.1016/j.ymeth.2019.04.017] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 04/06/2019] [Accepted: 04/25/2019] [Indexed: 01/19/2023] Open
Abstract
Monitoring extracellular pH (pHe) is important for biology understanding, since pHe and its homeostasis are closely relevant to cellular metabolism. Hydrogel-based pHe sensors have attracted significant attention and showed wide application, while they are tedious with significant time-cost operation and reproducibility variations for high-throughput application. Herein, we synthesized two polymers for pHe monitoring which are soluble in water at room temperature with easy operations and high reproducibility among various micro-plate wells for high-throughput analysis. P1 (P(OEGMA-co-MEO2MA-co-pHS)) and P2 (P(OEGMA-co-pHS)) were synthesized via the Reversible Addition Fragmentation Chain Transfer (RAFT) copolymerization of oligo(ethylene glycol) methacrylate (OEGMA), 2-(2'-methoxyethoxy) ethyl methacrylate (MEO2MA) and the pH sensitive fluorescence moiety N-fluoresceinyl methacrylamide (pHS). P1 is soluble in water at room temperature (25 °C) while insoluble at the temperature above 33 °C, indicating its feature of lower critical solution temperature (LCST) at 33 °C. Further P1 showed higher pH sensitivity and photostability than P2 (without LCST property) when used at physiological temperature (37 °C). Thus, P1 was chosen to in-situ monitor the micro-environmental acidification of E. coli, Hela and Ramos cells during their growth, and the metabolism inhibiting activity of a representative antibiotic, ampicillin. Cell concentration-dependent cellular acidification and drug concentration-dependent inhibition of cellular acidification were observed, demonstrating that the LCST polymer (P1) is suitable for real-time cellular acidification monitoring as well as for high-throughput drug screening. This study firstly demonstrated the use of a LCST polymeric sensor for high-throughput screening of antibiotics and investigation of cell metabolism.
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Affiliation(s)
- Tingting Pan
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Avenida da Universidade, Taipa, Macau, China; Department of Materials Science and Engineering, Southern University of Science and Technology, No 1088 Xueyuan Blvd, Xili, Nanshan District, Shenzhen, Guangdong 518055, China
| | - Cheng Yang
- Department of Materials Science and Engineering, Southern University of Science and Technology, No 1088 Xueyuan Blvd, Xili, Nanshan District, Shenzhen, Guangdong 518055, China
| | - Jiaze Li
- Department of Materials Science and Engineering, Southern University of Science and Technology, No 1088 Xueyuan Blvd, Xili, Nanshan District, Shenzhen, Guangdong 518055, China
| | - Jiapei Jiang
- Department of Materials Science and Engineering, Southern University of Science and Technology, No 1088 Xueyuan Blvd, Xili, Nanshan District, Shenzhen, Guangdong 518055, China
| | - Jiaxing Wen
- Department of Materials Science and Engineering, Southern University of Science and Technology, No 1088 Xueyuan Blvd, Xili, Nanshan District, Shenzhen, Guangdong 518055, China
| | - Zijin Wang
- Department of Materials Science and Engineering, Southern University of Science and Technology, No 1088 Xueyuan Blvd, Xili, Nanshan District, Shenzhen, Guangdong 518055, China
| | - Ke Zhong
- Department of Materials Science and Engineering, Southern University of Science and Technology, No 1088 Xueyuan Blvd, Xili, Nanshan District, Shenzhen, Guangdong 518055, China
| | - Yanqing Tian
- Department of Materials Science and Engineering, Southern University of Science and Technology, No 1088 Xueyuan Blvd, Xili, Nanshan District, Shenzhen, Guangdong 518055, China.
| | - Meiwan Chen
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Avenida da Universidade, Taipa, Macau, China.
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14
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Shamsipur M, Barati A, Nematifar Z. Fluorescent pH nanosensors: Design strategies and applications. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY C-PHOTOCHEMISTRY REVIEWS 2019. [DOI: 10.1016/j.jphotochemrev.2019.03.001] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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15
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Merino N, Aronson HS, Bojanova DP, Feyhl-Buska J, Wong ML, Zhang S, Giovannelli D. Living at the Extremes: Extremophiles and the Limits of Life in a Planetary Context. Front Microbiol 2019; 10:780. [PMID: 31037068 PMCID: PMC6476344 DOI: 10.3389/fmicb.2019.00780] [Citation(s) in RCA: 198] [Impact Index Per Article: 39.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 03/27/2019] [Indexed: 01/21/2023] Open
Abstract
Prokaryotic life has dominated most of the evolutionary history of our planet, evolving to occupy virtually all available environmental niches. Extremophiles, especially those thriving under multiple extremes, represent a key area of research for multiple disciplines, spanning from the study of adaptations to harsh conditions, to the biogeochemical cycling of elements. Extremophile research also has implications for origin of life studies and the search for life on other planetary and celestial bodies. In this article, we will review the current state of knowledge for the biospace in which life operates on Earth and will discuss it in a planetary context, highlighting knowledge gaps and areas of opportunity.
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Affiliation(s)
- Nancy Merino
- Department of Earth Sciences, University of Southern California, Los Angeles, CA, United States.,Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan.,Biosciences and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore National Lab, Livermore, CA, United States
| | - Heidi S Aronson
- Department of Biology, University of Southern California, Los Angeles, CA, United States
| | - Diana P Bojanova
- Department of Earth Sciences, University of Southern California, Los Angeles, CA, United States
| | - Jayme Feyhl-Buska
- Department of Earth Sciences, University of Southern California, Los Angeles, CA, United States
| | - Michael L Wong
- Department of Astronomy - Astrobiology Program, University of Washington, Seattle, WA, United States.,NASA Astrobiology Institute's Virtual Planetary Laboratory, University of Washington, Seattle, WA, United States
| | - Shu Zhang
- Section of Infection and Immunity, Herman Ostrow School of Dentistry of USC, University of Southern California, Los Angeles, CA, United States
| | - Donato Giovannelli
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan.,Department of Biology, University of Naples "Federico II", Naples, Italy.,Department of Marine and Coastal Science, Rutgers, The State University of New Jersey, New Brunswick, NJ, United States.,Institute for Biological Resources and Marine Biotechnology, National Research Council of Italy, Ancona, Italy
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16
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Abstract
Functional and genomic heterogeneity of individual cells are central players in a broad spectrum of normal and disease states. Our knowledge about the role of cellular heterogeneity in tissue and organism function remains limited due to analytical challenges one encounters when performing single cell studies in the context of cell-cell interactions. Information based on bulk samples represents ensemble averages over populations of cells, while data generated from isolated single cells do not account for intercellular interactions. We describe a new technology and demonstrate two important advantages over existing technologies: first, it enables multiparameter energy metabolism profiling of small cell populations (<100 cells)—a sample size that is at least an order of magnitude smaller than other, commercially available technologies; second, it can perform simultaneous real-time measurements of oxygen consumption rate (OCR), extracellular acidification rate (ECAR), and mitochondrial membrane potential (MMP)—a capability not offered by any other commercially available technology. Our results revealed substantial diversity in response kinetics of the three analytes in dysplastic human epithelial esophageal cells and suggest the existence of varying cellular energy metabolism profiles and their kinetics among small populations of cells. The technology represents a powerful analytical tool for multiparameter studies of cellular function.
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17
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Su F, Agarwal S, Pan T, Qiao Y, Zhang L, Shi Z, Kong X, Day K, Chen M, Meldrum D, Kodibagkar VD, Tian Y. Multifunctional PHPMA-Derived Polymer for Ratiometric pH Sensing, Fluorescence Imaging, and Magnetic Resonance Imaging. ACS APPLIED MATERIALS & INTERFACES 2018; 10:1556-1565. [PMID: 29210559 DOI: 10.1021/acsami.7b15796] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
In this paper, we report synthesis and characterization of a novel multimodality (MRI/fluorescence) probe for pH sensing and imaging. A multifunctional polymer was derived from poly(N-(2-hydroxypropyl)methacrylamide) (PHPMA) and integrated with a naphthalimide-based-ratiometric fluorescence probe and a gadolinium-1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid complex (Gd-DOTA complex). The polymer was characterized using UV-vis absorption spectrophotometry, fluorescence spectrofluorophotometry, magnetic resonance imaging (MRI), and confocal microscopy for optical and MRI-based pH sensing and cellular imaging. In vitro labeling of macrophage J774 and esophageal CP-A cell lines shows the polymer's ability to be internalized in the cells. The transverse relaxation time (T2) of the polymer was observed to be pH-dependent, whereas the spin-lattice relaxation time (T1) was not. The pH probe in the polymer shows a strong fluorescence-based ratiometric pH response with emission window changes, exhibiting blue emission under acidic conditions and green emission under basic conditions, respectively. This study provides new materials with multimodalities for pH sensing and imaging.
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Affiliation(s)
- Fengyu Su
- Center for Biosignatures Discovery Automation, Biodesign Institute, Arizona State University , Tempe, Arizona 85287, United States
| | - Shubhangi Agarwal
- School for Biological and Health Systems Engineering, Arizona State University , Tempe, Arizona 85281, United States
| | - Tingting Pan
- Department of Materials Science and Engineering, Southern University of Science and Technology , Shenzhen, Guangdong 518055, China
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau , Avenida da Universidade, Taipa, Macau 999078, China
| | - Yuan Qiao
- Department of Materials Science and Engineering, Southern University of Science and Technology , Shenzhen, Guangdong 518055, China
| | - Liqiang Zhang
- Center for Biosignatures Discovery Automation, Biodesign Institute, Arizona State University , Tempe, Arizona 85287, United States
| | - Zhengwei Shi
- Center for Biosignatures Discovery Automation, Biodesign Institute, Arizona State University , Tempe, Arizona 85287, United States
| | - Xiangxing Kong
- Center for Biosignatures Discovery Automation, Biodesign Institute, Arizona State University , Tempe, Arizona 85287, United States
| | - Kevin Day
- Center for Biosignatures Discovery Automation, Biodesign Institute, Arizona State University , Tempe, Arizona 85287, United States
| | - Meiwan Chen
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau , Avenida da Universidade, Taipa, Macau 999078, China
| | - Deirdre Meldrum
- Center for Biosignatures Discovery Automation, Biodesign Institute, Arizona State University , Tempe, Arizona 85287, United States
| | - Vikram D Kodibagkar
- School for Biological and Health Systems Engineering, Arizona State University , Tempe, Arizona 85281, United States
| | - Yanqing Tian
- Department of Materials Science and Engineering, Southern University of Science and Technology , Shenzhen, Guangdong 518055, China
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18
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Someya D, Arai S, Fujie T, Takeoka S. Extracellular pH imaging of a plant leaf with a polyelectrolyte multilayered nanosheet. RSC Adv 2018; 8:35651-35657. [PMID: 35547891 PMCID: PMC9087818 DOI: 10.1039/c8ra06308g] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 10/07/2018] [Indexed: 01/15/2023] Open
Abstract
We have developed a sheet-like pH imaging sensor based on a flexible and physically adhesive polymer thin film (referred to as a “pH sensing nanosheet”). The pH sensing nanosheet was composed of two films: one is a pH-sensitive layer-by-layer (LbL) film constructed from fluorescein-conjugated poly(acrylic acid) and poly(allylamine hydrochloride) and the other is a pH-insensitive film made from Nile red-embedded poly(d,l-lactic acid). The pH sensing nanosheet enabled the ratiometric imaging of pH changes in a leaf (500 × 500 μm2), namely the apoplastic ion milieu responding to an external NaCl stress. It was successfully mapped out that the alkalization of the leaf apoplast spread from the leaf base to the tip at 20 min after the stimulation and the pH value increased up to approximately pH 6.3 from less than pH 4.5 within 60 min when a 100 mM NaCl aqueous solution was added. The pH sensing nanosheet should be useful for energy metabolic mapping in tissue biology. We have developed a sheet-like pH imaging sensor based on a flexible and physically adhesive polymer thin film (referred to as a “pH sensing nanosheet”).![]()
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Affiliation(s)
- Daichi Someya
- Department of Life Science and Medical Bioscience
- Waseda University
- Tokyo 162-8480
- Japan
| | - Satoshi Arai
- PRIME
- Japan Agency for Medical Research and Development (AMED)
- Tokyo 100-0004
- Japan
- Research Institute for Science and Engineering
| | - Toshinori Fujie
- Waseda Institute for Advanced Study
- Waseda University
- Tokyo 162-8480
- Japan
- Japan Science and Technology Agency
| | - Shinji Takeoka
- Department of Life Science and Medical Bioscience
- Waseda University
- Tokyo 162-8480
- Japan
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19
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Affiliation(s)
- Yanan Liu
- College of Chemistry and Pharmaceutical Science; Qingdao Agricultural University; 266109 Qingdao People's Republic of China
| | - Zuwei Song
- College of Chemistry and Pharmaceutical Science; Qingdao Agricultural University; 266109 Qingdao People's Republic of China
| | - Libin Gao
- College of Chemistry and Pharmaceutical Science; Qingdao Agricultural University; 266109 Qingdao People's Republic of China
| | - Jianzhong Li
- College of Chemistry and Pharmaceutical Science; Qingdao Agricultural University; 266109 Qingdao People's Republic of China
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20
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Su F, Zhang L, Kong X, Lee F, Tian Y, Meldrum DR. Ratiometric glucose sensing based on fluorescent oxygen films and glucose oxidase. SENSING AND BIO-SENSING RESEARCH 2017. [DOI: 10.1016/j.sbsr.2017.03.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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21
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Liu J, Zhang S, Zhang C, Dong J, Shen C, Zhu J, Xu H, Fu M, Yang G, Zhang X. A water-soluble two-photon ratiometric triarylboron probe with nucleolar targeting by preferential RNA binding. Chem Commun (Camb) 2017; 53:11476-11479. [DOI: 10.1039/c7cc06045a] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
By functionalizing triarylboron with cyclen, we developed a water-soluble two-photon ratiometric triarylboron probe with nucleolar targeting by preferential RNA binding.
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