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Smith RL, England A, Millis J, Hirn C, Collins SD, Connell LB. A Microfabricated, Flow-Driven Grinding Mill for Mechanical Cell Lysing. Anal Chem 2023; 95:17494-17501. [PMID: 37976075 DOI: 10.1021/acs.analchem.3c02344] [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: 11/19/2023]
Abstract
This paper presents the design, microfabrication, and demonstration of a novel microfluidic grinding mill for the lysis of the dinoflagellate, Alexandrium, a neurotoxin-producing genus of algae that is responsible for red tide and paralytic shellfish poisoning. The mill consists of a high-speed, hydrodynamically driven microrotor coupled to a micro grinding mill that lyses robust algal cells by mechanical abrasion with single-pass efficiencies as high as 97%. These efficiencies are comparable to, or better than, current mechanical and chemical lysing methods without adding complications associated with harsh chemical additives that can interfere with subsequent downstream bioanalysis. Release of cytoplasm from lysed algae was confirmed using polymerase chain reaction (PCR) amplification of Alexandrium DNA using dinoflagellate primers.
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Affiliation(s)
| | - Avery England
- Department of Chemsitry, University of Maine, Orono, Maine 04469, United States
| | | | - Corey Hirn
- School of Marine Science, University of Maine, Orono, Maine 04469, United States
| | - Scott D Collins
- Department of Chemsitry, University of Maine, Orono, Maine 04469, United States
| | - Laurie B Connell
- School of Marine Science, University of Maine, Orono, Maine 04469, United States
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2
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Lad SB, Roy S, George JE, Chakraborti H, Lalsare S, Barik B, Singh A, Zade A, Agrawal S, Shastri J, Chatterjee A, Das Gupta K, Paul D, Kondabagil K. Development of a PNA–DiSc 2 based portable absorbance platform for the detection of pathogen nucleic acids. Analyst 2022; 147:5306-5313. [DOI: 10.1039/d2an01351g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
A PortAbs based pathogen nucleic acid detection system using peptide nucleic acid (PNA) and a cyanine dye, DiSc2(5). The shift is measured of the absorbance induced by binding of a PNA probe to a complementary DNA strand using a portable two-color absorption system.
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Affiliation(s)
- Shailesh B. Lad
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Shomdutta Roy
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Jijo Easo George
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Himadri Chakraborti
- Department of Physics, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Saumitra Lalsare
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Bikash Barik
- Department of Physics, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Arushi Singh
- Department of Physics, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Amrutraj Zade
- Haystack Analytics Pvt. Ltd. Society For Innovation & Entrepreneurship (SINE), Kanwal Rekhi Building, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Sachee Agrawal
- Molecular Diagnostic Reference Laboratory, Kasturba Hospital for Infectious Diseases, Mumbai, India
| | - Jayanthi Shastri
- Molecular Diagnostic Reference Laboratory, Kasturba Hospital for Infectious Diseases, Mumbai, India
| | - Anirvan Chatterjee
- Haystack Analytics Pvt. Ltd. Society For Innovation & Entrepreneurship (SINE), Kanwal Rekhi Building, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Kantimay Das Gupta
- Department of Physics, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Debjani Paul
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Kiran Kondabagil
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
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3
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Rolling Circle Amplification as an Efficient Analytical Tool for Rapid Detection of Contaminants in Aqueous Environments. BIOSENSORS-BASEL 2021; 11:bios11100352. [PMID: 34677308 PMCID: PMC8533700 DOI: 10.3390/bios11100352] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 09/16/2021] [Accepted: 09/21/2021] [Indexed: 12/16/2022]
Abstract
Environmental contaminants are a global concern, and an effective strategy for remediation is to develop a rapid, on-site, and affordable monitoring method. However, this remains challenging, especially with regard to the detection of various contaminants in complex water environments. The application of molecular methods has recently attracted increasing attention; for example, rolling circle amplification (RCA) is an isothermal enzymatic process in which a short nucleic acid primer is amplified to form a long single-stranded nucleic acid using a circular template and special nucleic acid polymerases. Furthermore, this approach can be further engineered into a device for point-of-need monitoring of environmental pollutants. In this paper, we describe the fundamental principles of RCA and the advantages and disadvantages of RCA assays. Then, we discuss the recently developed RCA-based tools for environmental analysis to determine various targets, including heavy metals, organic small molecules, nucleic acids, peptides, proteins, and even microorganisms in aqueous environments. Finally, we summarize the challenges and outline strategies for the advancement of this technique for application in contaminant monitoring.
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Miltsov S, Alonso‐Chamarro J, Puyol M. Synthesis and optical characterization of new ketocyanine dyes with extended polymethine chaines. J Heterocycl Chem 2020. [DOI: 10.1002/jhet.4027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Sergey Miltsov
- Institute of Macromolecular CompoundsRussian Academy of Sciences St. Petersburg Russia
| | - Julian Alonso‐Chamarro
- Grup de Sensors i Biosensors, Unitat de Quimica Analítica, Facultat de CiènciesUniversitat Autònoma de Barcelona Bellaterra Spain
| | - Mar Puyol
- Grup de Sensors i Biosensors, Unitat de Quimica Analítica, Facultat de CiènciesUniversitat Autònoma de Barcelona Bellaterra Spain
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Abstract
With the rapid development of high technology, chemical science is not as it used to be a century ago. Many chemists acquire and utilize skills that are well beyond the traditional definition of chemistry. The digital age has transformed chemistry laboratories. One aspect of this transformation is the progressing implementation of electronics and computer science in chemistry research. In the past decade, numerous chemistry-oriented studies have benefited from the implementation of electronic modules, including microcontroller boards (MCBs), single-board computers (SBCs), professional grade control and data acquisition systems, as well as field-programmable gate arrays (FPGAs). In particular, MCBs and SBCs provide good value for money. The application areas for electronic modules in chemistry research include construction of simple detection systems based on spectrophotometry and spectrofluorometry principles, customizing laboratory devices for automation of common laboratory practices, control of reaction systems (batch- and flow-based), extraction systems, chromatographic and electrophoretic systems, microfluidic systems (classical and nonclassical), custom-built polymerase chain reaction devices, gas-phase analyte detection systems, chemical robots and drones, construction of FPGA-based imaging systems, and the Internet-of-Chemical-Things. The technology is easy to handle, and many chemists have managed to train themselves in its implementation. The only major obstacle in its implementation is probably one's imagination.
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Affiliation(s)
- Gurpur Rakesh D Prabhu
- Department of Chemistry, National Tsing Hua University, 101, Section 2, Kuang-Fu Road, Hsinchu, 30013, Taiwan.,Department of Applied Chemistry, National Chiao Tung University, 1001 University Road, Hsinchu, 300, Taiwan
| | - Pawel L Urban
- Department of Chemistry, National Tsing Hua University, 101, Section 2, Kuang-Fu Road, Hsinchu, 30013, Taiwan.,Frontier Research Center on Fundamental and Applied Sciences of Matters, National Tsing Hua University, 101, Section 2, Kuang-Fu Road, Hsinchu, 30013, Taiwan
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6
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Ebelt ND, Manuel ER. Utilizing Salmonella to treat solid malignancies. J Surg Oncol 2017; 116:75-82. [PMID: 28420039 DOI: 10.1002/jso.24644] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Accepted: 03/22/2017] [Indexed: 12/18/2022]
Abstract
Despite intensive research into novel treatment strategies for cancer, it remains the second most common cause of death in industrialized populations. Pancreatic ductal adenocarcinoma (PDAC) is a highly aggressive disease with dismal prognosis. Currently, surgical resection offers the best chance for extended survival, yet recurrence remains high and is associated with poor outcome. Systemic treatment has evolved from non-specific, cytotoxic chemotherapy to the use of cancer-targeting agents, profoundly changing treatment approaches in the metastatic and adjuvant settings. One promising approach, highlighted in this review, uses the inherent capacity of Salmonella to colonize and eliminate solid tumors.
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Affiliation(s)
- Nancy D Ebelt
- Department of Experimental Therapeutics, Beckman Research Institute of City of Hope, Duarte, California
| | - Edwin R Manuel
- Department of Experimental Therapeutics, Beckman Research Institute of City of Hope, Duarte, California
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Bazin I, Tria SA, Hayat A, Marty JL. New biorecognition molecules in biosensors for the detection of toxins. Biosens Bioelectron 2016; 87:285-298. [PMID: 27568847 DOI: 10.1016/j.bios.2016.06.083] [Citation(s) in RCA: 105] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Revised: 06/17/2016] [Accepted: 06/28/2016] [Indexed: 12/24/2022]
Abstract
Biological and synthetic recognition elements are at the heart of the majority of modern bioreceptor assays. Traditionally, enzymes and antibodies have been integrated in the biosensor designs as a popular choice for the detection of toxin molecules. But since 1970s, alternative biological and synthetic binders have been emerged as a promising alternative to conventional biorecognition elements in detection systems for laboratory and field-based applications. Recent research has witnessed immense interest in the use of recombinant enzymatic methodologies and nanozymes to circumvent the drawbacks associated with natural enzymes. In the area of antibody production, technologies based on the modification of in vivo synthesized materials and in vitro approaches with development of "display "systems have been introduced in the recent years. Subsequently, molecularly-imprinted polymers and Peptide nucleic acid (PNAs) were developed as an attractive receptor with applications in the area of sample preparation and detection systems. In this article, we discuss all alternatives to conventional biomolecules employed in the detection of various toxin molecules We review recent developments in modified enzymes, nanozymes, nanobodies, aptamers, peptides, protein scaffolds and DNazymes. With the advent of nanostructures and new interface materials, these recognition elements will be major players in future biosensor development.
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Affiliation(s)
- Ingrid Bazin
- École des Mines d'Alès, 6 Avenuede Clavières, 30100 Alès Cedex, France.
| | - Scherrine A Tria
- École des Mines d'Alès, 6 Avenuede Clavières, 30100 Alès Cedex, France
| | - Akhtar Hayat
- BAE (Biocapteurs-Analyses-Environnement), Universite de Perpignan Via Domitia, 52 Avenue Paul Alduy, Perpignan Cedex 66860, France; Interdisciplinary Research Centre in Biomedical Materials (IRCBM), COMSATS Institute of Information Technology (CIIT), Lahore, Pakistan
| | - Jean-Louis Marty
- BAE (Biocapteurs-Analyses-Environnement), Universite de Perpignan Via Domitia, 52 Avenue Paul Alduy, Perpignan Cedex 66860, France
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8
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A label-free colorimetric assay for detection of c-Myc mRNA based on peptide nucleic acid and silver nanoparticles. Sci Bull (Beijing) 2016. [DOI: 10.1007/s11434-016-1004-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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9
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Multiplexed hydrogel microparticle suspension arrays for facile ribosomal RNA integrity assays. BIOTECHNOL BIOPROC E 2015. [DOI: 10.1007/s12257-015-0265-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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10
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Abstract
This minireview discusses universal electronic modules (generic programmable units) and their use by analytical chemists to construct inexpensive, miniature or automated devices. Recently, open-source platforms have gained considerable popularity among tech-savvy chemists because their implementation often does not require expert knowledge and investment of funds. Thus, chemistry students and researchers can easily start implementing them after a few hours of reading tutorials and trial-and-error. Single-board microcontrollers and micro-computers such as Arduino, Teensy, Raspberry Pi or BeagleBone enable collecting experimental data with high precision as well as efficient control of electric potentials and actuation of mechanical systems. They are readily programmed using high-level languages, such as C, C++, JavaScript or Python. They can also be coupled with mobile consumer electronics, including smartphones as well as teleinformatic networks. More demanding analytical tasks require fast signal processing. Field-programmable gate arrays enable efficient and inexpensive prototyping of high-performance analytical platforms, thus becoming increasingly popular among analytical chemists. This minireview discusses the advantages and drawbacks of universal electronic modules, considering their application in prototyping and manufacture of intelligent analytical instrumentation.
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Affiliation(s)
- Pawel L Urban
- Department of Applied Chemistry, National Chiao Tung University, Hsinchu 300, Taiwan
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11
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Cunha MV, Inácio J. Nucleic-acid testing, new platforms and nanotechnology for point-of-decision diagnosis of animal pathogens. Methods Mol Biol 2015; 1247:253-83. [PMID: 25399103 PMCID: PMC7122192 DOI: 10.1007/978-1-4939-2004-4_20] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Accurate disease diagnosis in animals is crucial for animal well-being but also for preventing zoonosis transmission to humans. In particular, livestock diseases may constitute severe threats to humans due to the particularly high physical contact and exposure and, also, be the cause of important economic losses, even in non-endemic countries, where they often arise in the form of rapid and devastating epidemics. Rapid diagnostic tests have been used for a long time in field situations, particularly during outbreaks. However, they mostly rely on serological approaches, which may confirm the exposure to a particular pathogen but may be inappropriate for point-of-decision (point-of-care) settings when emergency responses supported on early and accurate diagnosis are required. Moreover, they often exhibit modest sensitivity and hence significantly depend on later result confirmation in central or reference laboratories. The impressive advances observed in recent years in materials sciences and in nanotechnology, as well as in nucleic-acid synthesis and engineering, have led to an outburst of new in-the-bench and prototype tests for nucleic-acid testing towards point-of-care diagnosis of genetic and infectious diseases. Manufacturing, commercial, regulatory, and technical nature issues for field applicability more likely have hindered their wider entrance into veterinary medicine and practice than have fundamental science gaps. This chapter begins by outlining the current situation, requirements, difficulties, and perspectives of point-of-care tests for diagnosing diseases of veterinary interest. Nucleic-acid testing, particularly for the point of care, is addressed subsequently. A range of valuable signal transduction mechanisms commonly employed in proof-of-concept schemes and techniques born on the analytical chemistry laboratories are also described. As the essential core of this chapter, sections dedicated to the principles and applications of microfluidics, lab-on-a-chip, and nanotechnology for the development of point-of-care tests are presented. Microdevices already applied or under development for application in field diagnosis of animal diseases are reviewed.
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Affiliation(s)
- Mónica V. Cunha
- Instituto Nacional de Investigação Agrária e Veterinária, IP and Centro de Biologia Ambiental, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
| | - João Inácio
- Instituto Nacional de Investigação Agrária e Veterinária, IP, Lisboa, Portugal and School of Pharmacy and Biomolecular Sciences, University of Brighton, Brighton, United Kingdom
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Approaches for the detection of harmful algal blooms using oligonucleotide interactions. Anal Bioanal Chem 2014; 407:95-116. [PMID: 25381608 DOI: 10.1007/s00216-014-8193-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Revised: 09/02/2014] [Accepted: 09/15/2014] [Indexed: 01/14/2023]
Abstract
Blooms of microscopic algae in our waterways are becoming an increasingly important environmental concern. Many are sources of harmful biotoxins that can lead to death in humans, marine life and birds. Additionally, their biomass can cause damage to ecosystems such as oxygen depletion, displacement of species and habitat alteration. Globally, the number and frequency of harmful algal blooms has increased over the last few decades, and monitoring and detection strategies have become essential for managing these events. This review discusses developments in the use of oligonucleotide-based 'molecular probes' for the selective monitoring of algal cell numbers. Specifically, hybridisation techniques will be a focus.
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