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Garcia A, Grundmann O. The Utilization and Development of Viral Vectors in Vaccines as a Prophylactic Treatment Against Ebola Virus as an Emerging and Zoonotic Infectious Disease. Mini Rev Med Chem 2024; 24:289-299. [PMID: 37489781 DOI: 10.2174/1389557523666230725115324] [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: 12/12/2022] [Revised: 02/26/2023] [Accepted: 03/15/2023] [Indexed: 07/26/2023]
Abstract
Alongside the prescription of commonly used antivirals, such as acyclovir, remdesivir, oseltamivir, and ciprofloxacin, the most efficient way to prevent or treat communicable diseases is by vaccination. Vaccines have been the most efficient way to prevent or treat highly transmissible infectious agents, such as Ebola, Anthrax, and Dengue Fever. Most epidemics of these highly transmissible infectious agents occur in places, such as South America, Central America, Tropical Asia, and Africa, where the availability of resources and access to adequate healthcare are limited. However, recent events in history have proven that even with access to resources and proper healthcare, those in firstworld countries are not invincible when it comes to infectious diseases and epidemics. The Ebola virus outbreak in West Africa highlighted the gaps in therapeutic advancement and readiness and led to the rapid development of novel vaccine approaches. Viral vectors, in the case of the Ebola vaccine the Vesicular Stomatitis Virus (VSV), can be safely used to activate or initiate the innate adaptive immune response to protect against viral infection. When developed properly and with extensive study, novel vaccine approaches allow physicians and health experts to control the rate at which viruses spread or prevent transmission. This review will discuss the advantages of viral vector vaccines, their chemistry and development, and the pathophysiology of the Ebola virus to develop advantageous and efficacious treatments.
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Affiliation(s)
- Anthony Garcia
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, 1345 Center Drive, Room P3-20, Gainesville, FL 32611, USA
| | - Oliver Grundmann
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, 1345 Center Drive, Room P3-20, Gainesville, FL 32611, USA
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2
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Kachwala MJ, Smith CW, Nandu N, Yigit MV. Recombinase amplified CRISPR enhanced chain reaction (RACECAR) for viral genome detection. NANOSCALE 2022; 14:13500-13504. [PMID: 36102688 PMCID: PMC9623498 DOI: 10.1039/d2nr03590a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
We have developed a 'recombinase amplified CRISPR enhanced chain reaction' (RACECAR) assay that can detect as little as 40 copies of hepatitis B virus (HBV) genome using a benchtop spectrofluorometer. The limit of detection was determined to be 3 copies of HBV genome. The specificity of RACECAR was confirmed against hepatitis A virus (HAV). This assay can detect the genomic targets directly in serum samples without an extraction step. The 4 h-long fluorometric assay was developed by combining three tiers of isothermal amplification processes and can be repurposed for any target of choice. This highly modular reaction setup is an untapped resource that can be incorporated into the front-runners of molecular diagnostics.
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Affiliation(s)
- Mahera J Kachwala
- Department of Chemistry, University at Albany, State University of New York, 1400 Washington Avenue, Albany, New York 12222, USA.
| | - Christopher W Smith
- Department of Chemistry, University at Albany, State University of New York, 1400 Washington Avenue, Albany, New York 12222, USA.
| | - Nidhi Nandu
- Department of Chemistry, University at Albany, State University of New York, 1400 Washington Avenue, Albany, New York 12222, USA.
| | - Mehmet V Yigit
- Department of Chemistry, University at Albany, State University of New York, 1400 Washington Avenue, Albany, New York 12222, USA.
- The RNA Institute, University at Albany, State University of New York, 1400 Washington Avenue, Albany, New York 12222, USA
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Kumar N, Rana M, Geiwitz M, Khan NI, Catalano M, Ortiz-Marquez JC, Kitadai H, Weber A, Dweik B, Ling X, van Opijnen T, Argun AA, Burch KS. Rapid, Multianalyte Detection of Opioid Metabolites in Wastewater. ACS NANO 2022; 16:3704-3714. [PMID: 35201755 PMCID: PMC9949512 DOI: 10.1021/acsnano.1c07094] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
By monitoring opioid metabolites, wastewater-based epidemiology (WBE) could be an excellent tool for real-time information on the consumption of illicit drugs. A key limitation of WBE is the reliance on costly laboratory-based techniques that require substantial infrastructure and trained personnel, resulting in long turnaround times. Here, we present an aptamer-based graphene field effect transistor (AptG-FET) platform for simultaneous detection of three different opioid metabolites. This platform provides a reliable, rapid, and inexpensive method for quantitative analysis of opioid metabolites in wastewater. The platform delivers a limit of detection 2-3 orders of magnitude lower than previous reports, but in line with the concentration range (pg/mL to ng/mL) of these opioid metabolites present in real samples. To enable multianalyte detection, we developed a facile, reproducible, and high-yield fabrication process producing 20 G-FETs with integrated side gate platinum (Pt) electrodes on a single chip. Our devices achieved the selective multianalyte detection of three different metabolites: noroxycodone (NX), 2-ethylidene-1,5-dimethyl-3,3-diphenylpyrrolidine (EDDP), and norfentanyl (NF) in wastewater diluted 20× in buffer.
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Affiliation(s)
- Narendra Kumar
- Department of Physics, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | - Muhit Rana
- Giner Inc., Newton, Massachusetts 02466, United States
| | - Michael Geiwitz
- Department of Physics, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | | | - Matthew Catalano
- Department of Physics, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | - Juan C Ortiz-Marquez
- Department of Biology, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | - Hikari Kitadai
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, United States
| | - Andrew Weber
- Giner Inc., Newton, Massachusetts 02466, United States
| | - Badawi Dweik
- Giner Inc., Newton, Massachusetts 02466, United States
| | - Xi Ling
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, United States
| | - Tim van Opijnen
- Department of Biology, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | - Avni A Argun
- Giner Inc., Newton, Massachusetts 02466, United States
| | - Kenneth S Burch
- Department of Physics, Boston College, Chestnut Hill, Massachusetts 02467, United States
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Portable Au Nanoparticle-Based Colorimetric Sensor Strip for Rapid On-Site Detection of Cd2+ Ions in Potable Water. BIOCHIP JOURNAL 2021. [DOI: 10.1007/s13206-021-00029-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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5
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Minakshi P, Ghosh M, Kumar R, Brar B, Lambe UP, Banerjee S, Ranjan K, Kumar B, Goel P, Malik YS, Prasad G. An Insight into Nanomedicinal Approaches to Combat Viral Zoonoses. Curr Top Med Chem 2021; 20:915-962. [PMID: 32209041 DOI: 10.2174/1568026620666200325114400] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 12/31/2019] [Accepted: 12/31/2019] [Indexed: 12/12/2022]
Abstract
BACKGROUND Emerging viral zoonotic diseases are one of the major obstacles to secure the "One Health" concept under the current scenario. Current prophylactic, diagnostic and therapeutic approaches often associated with certain limitations and thus proved to be insufficient for customizing rapid and efficient combating strategy against the highly transmissible pathogenic infectious agents leading to the disastrous socio-economic outcome. Moreover, most of the viral zoonoses originate from the wildlife and poor knowledge about the global virome database renders it difficult to predict future outbreaks. Thus, alternative management strategy in terms of improved prophylactic vaccines and their delivery systems; rapid and efficient diagnostics and effective targeted therapeutics are the need of the hour. METHODS Structured literature search has been performed with specific keywords in bibliographic databases for the accumulation of information regarding current nanomedicine interventions along with standard books for basic virology inputs. RESULTS Multi-arrayed applications of nanomedicine have proved to be an effective alternative in all the aspects regarding the prevention, diagnosis, and control of zoonotic viral diseases. The current review is focused to outline the applications of nanomaterials as anti-viral vaccines or vaccine/drug delivery systems, diagnostics and directly acting therapeutic agents in combating the important zoonotic viral diseases in the recent scenario along with their potential benefits, challenges and prospects to design successful control strategies. CONCLUSION This review provides significant introspection towards the multi-arrayed applications of nanomedicine to combat several important zoonotic viral diseases.
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Affiliation(s)
- Prasad Minakshi
- Department of Animal Biotechnology, LLR University of Veterinary and Animal Sciences, Hisar-125001, Haryana, 125004, India
| | - Mayukh Ghosh
- Department of Veterinary Physiology and Biochemistry, RGSC, Banaras Hindu University, Mirzapur (UP) - 231001, India
| | - Rajesh Kumar
- Department of Veterinary Physiology and Biochemistry, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar-125001, Haryana, 125004, India
| | - Basanti Brar
- Department of Animal Biotechnology, LLR University of Veterinary and Animal Sciences, Hisar-125001, Haryana, 125004, India
| | - Upendra P Lambe
- Department of Animal Biotechnology, LLR University of Veterinary and Animal Sciences, Hisar-125001, Haryana, 125004, India
| | - Somesh Banerjee
- Department of Veterinary Microbiology, Immunology Section, LUVAS, Hisar-125004, India
| | - Koushlesh Ranjan
- Department of Veterinary Physiology and Biochemistry, Sardar Vallabhbhai Patel University of Agriculture and Technology, Meerut, 250110, India
| | | | - Parveen Goel
- Department of Veterinary Medicine, LLR University of Veterinary and Animal Sciences, Hisar, Haryana, 125004, India
| | - Yashpal S Malik
- Division of Standardisation, Indian Veterinary Research Institute Izatnagar - Bareilly (UP) - 243122, India
| | - Gaya Prasad
- Sardar Vallabhbhai Patel University of Agriculture and Technology, Meerut, UP, 250110, India
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Kachwala MJ, Smith CW, Nandu N, Yigit MV. Reprogrammable Gel Electrophoresis Detection Assay Using CRISPR-Cas12a and Hybridization Chain Reaction. Anal Chem 2021; 93:1934-1938. [PMID: 33404234 DOI: 10.1021/acs.analchem.0c04949] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Hybridization chain reaction (HCR) is a DNA-based target-induced cascade reaction. Due to its unique enzyme-free amplification feature, HCR is often employed for sensing applications. Much like DNA nanostructures that have been designed to respond to a specific stimulus, HCR employs nucleic acids that reconfigure and assemble in the presence of a specific trigger. Despite its standalone capabilities, HCR is highly modular; therefore, it can be advanced and repurposed when coupled with latest discoveries. To this effect, we have developed a gel electrophoresis-based detection approach which combines the signal amplification feature of HCR with the programmability and sensitivity of the CRISPR-Cas12a system. By incorporating CRISPR-Cas12a, we have achieved greater sensitivity and reversed the signal output from TURN OFF to TURN ON. CRISPR-Cas12a also enabled us to rapidly reprogram the assay for the detection of both ssDNA and dsDNA target sequences by replacing a single reaction component in the detection kit. Detection of conserved, both ssDNA and dsDNA, regions of tobacco curly shoot virus (TCSV) and hepatitis B virus (HepBV) genomes is demonstrated with this methodology. This low-cost gel electrophoresis assay can detect as little as 1.5 fmol of the target without any additional target amplification steps and is about 100-fold more sensitive than HCR-alone approach.
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Affiliation(s)
- Mahera J Kachwala
- Department of Chemistry, University at Albany, State University of New York, 1400 Washington Avenue, Albany, New York 12222, United States
| | - Christopher W Smith
- Department of Chemistry, University at Albany, State University of New York, 1400 Washington Avenue, Albany, New York 12222, United States
| | - Nidhi Nandu
- Department of Chemistry, University at Albany, State University of New York, 1400 Washington Avenue, Albany, New York 12222, United States
| | - Mehmet V Yigit
- Department of Chemistry, University at Albany, State University of New York, 1400 Washington Avenue, Albany, New York 12222, United States.,The RNA Institute, University at Albany, State University of New York, 1400 Washington Avenue, Albany, New York 12222, United States
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Wang Y, Kong SL, Su XD. A centrifugation-assisted visual detection of SNP in circulating tumor DNA using gold nanoparticles coupled with isothermal amplification. RSC Adv 2020; 10:1476-1483. [PMID: 35494678 PMCID: PMC9047361 DOI: 10.1039/c9ra09029k] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Accepted: 12/18/2019] [Indexed: 11/30/2022] Open
Abstract
Detection of single-nucleotide polymorphism (SNP) in circulating tumor DNA (ctDNA) is challenging because of the large DNA fragmentation (∼150 nt) and the strong background of normal cell free DNA (cfDNA). Here we developed a rapid centrifugation-assisted colorimetric assay using gold nanoparticles (AuNPs) coupled with isothermal amplification to detect a SNP (G to C mutation) in KRAS, p.G13D in ctDNA. Compared to conventional AuNP aggregation assays, our assay contains four unique design concepts. Firstly, a centrifugation step is introduced at the end of the reaction that significantly enhances the colorimetric readout by providing visually distinct precipitation for the SNP ctDNA. Secondly, to achieve a fast turnover rate for clinical pM demand, a “critical linker concentration” concept is introduced to the assay. Thirdly, in order to achieve an unambiguous differentiation of the SNP ctDNA from wild type cfDNA and the control sample without DNA, a “color code conversion” strategy is employed, where a complementary sequence of the linker DNA is introduced to manipulate the AuNP aggregation. Finally, ethylenediaminetetraacetic acid is used for enzyme inactivation only at room temperature while stabilizing the AuNP solution from unwanted aggregation. Our assay coupling two amplification strategies (isothermal amplification and centrifugation-assisted assembly) is capable of both quantitative and qualitative differentiation of SNP in ctDNA of ∼150 nt at a clinically relevant concentration and 67 pM limit of detection and in the presence of 99% normal cfDNA background. This assay can be used for point-of-care colon cancer diagnosis and prognosis with a fast turnover time (<2 h). A centrifugation-assisted dual signal amplified visual detection of ctDNA SNP (∼150 nt, 1% clinic sensitivity) within 2 hours has been reported.![]()
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Affiliation(s)
- Yusong Wang
- Institute of Materials Research and Engineering (IMRE)
- Agency for Science, Technology and Research (A*STAR)
- Singapore 138634
| | - Say Li Kong
- Genome Institute of Singapore (GIS)
- Agency for Science, Technology and Research (A*STAR)
- Singapore 138672
| | - Xiao Di Su
- Institute of Materials Research and Engineering (IMRE)
- Agency for Science, Technology and Research (A*STAR)
- Singapore 138634
- Department of Chemistry
- National University of Singapore
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Abstract
Viruses, which are the most abundant biological entities on the planet, have been regarded as the "dark matter" of biology in the sense that despite their ubiquity and frequent presence in large numbers, their detection and analysis are not always straightforward. The majority of them are very small (falling under the limit of 0.5 μm), and collectively, they are extraordinarily diverse. In fact, the majority of the genetic diversity on the planet is found in the so-called virosphere, or the world of viruses. Furthermore, the most frequent viral agents of disease in humans display an RNA genome, and frequently evolve very fast, due to the fact that most of their polymerases are devoid of proofreading activity. Therefore, their detection, genetic characterization, and epidemiological surveillance are rather challenging. This review (part of the Curated Collection on Advances in Molecular Epidemiology of Infectious Diseases) describes many of the methods that, throughout the last few decades, have been used for viral detection and analysis. Despite the challenge of having to deal with high genetic diversity, the majority of these methods still depend on the amplification of viral genomic sequences, using sequence-specific or sequence-independent approaches, exploring thermal profiles or a single nucleic acid amplification temperature. Furthermore, viral populations, and especially those with RNA genomes, are not usually genetically uniform but encompass swarms of genetically related, though distinct, viral genomes known as viral quasispecies. Therefore, sequence analysis of viral amplicons needs to take this fact into consideration, as it constitutes a potential analytic problem. Possible technical approaches to deal with it are also described here. *This article is part of a curated collection.
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Nandu N, Hizir MS, Yigit MV. Systematic Investigation of Two-Dimensional DNA Nanoassemblies for Construction of a Nonspecific Sensor Array. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:14983-14992. [PMID: 29739192 DOI: 10.1021/acs.langmuir.8b00788] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
We have performed a systematic study to analyze the effect of ssDNA length, nucleobase composition, and the type of two-dimensional nanoparticles (2D-nps) on the desorption response of 36 two-dimensional nanoassemblies (2D-NAs) against several proteins. The studies were performed using fluorescently labeled polyA, polyC, and polyT with 23, 18, 12, and 7 nucleotide-long sequences. The results suggest that the ssDNAs with polyC and longer sequences are more resistant to desorption, compared to their counterparts. In addition, 2D-NAs assembled using WS2 were least susceptible to desorption by the proteins tested, whereas nGO 2D-NAs were the most susceptible nanoassemblies. Later, the results of these systematic studies were used to construct a sensor array for discrimination of seven model proteins (BSA, lipase, alkaline phosphatase, acid phosphatase, protease, β-galactosidase, and Cytochrome c). Neither the ssDNAs nor the 2D-nps have any specific interaction with the proteins tested. Only the displacement of the ssDNAs from the 2D-np surface was measured upon the disruption of the existing forces within 2D-NAs. A customized sensor array with five 2D-NAs was developed as a result of a careful screening/filtering process. The sensor array was tested against 200 nM of protein targets, and each protein was discriminated successfully. The results suggest that the systematic studies performed using various ssDNAs and 2D-nps enabled the construction of a sensor array without a bind-and-release sensing mechanism. The studies also demonstrate the significance of systematic investigations in the construction of two-dimensional DNA nanoassemblies for functional studies.
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Affiliation(s)
- Nidhi Nandu
- Department of Chemistry , University at Albany, State University of New York , 1400 Washington Avenue , Albany , New York 12222 , United States
| | - Mustafa Salih Hizir
- Department of Chemistry , University at Albany, State University of New York , 1400 Washington Avenue , Albany , New York 12222 , United States
| | - Mehmet V Yigit
- Department of Chemistry , University at Albany, State University of New York , 1400 Washington Avenue , Albany , New York 12222 , United States
- The RNA Institute , University at Albany, State University of New York , 1400 Washington Avenue , Albany , New York 12222 , United States
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Augspurger EE, Rana M, Yigit MV. Chemical and Biological Sensing Using Hybridization Chain Reaction. ACS Sens 2018; 3:878-902. [PMID: 29733201 DOI: 10.1021/acssensors.8b00208] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Since the advent of its theoretical discovery more than 30 years ago, DNA nanotechnology has been used in a plethora of diverse applications in both the fundamental and applied sciences. The recent prominence of DNA-based technologies in the scientific community is largely due to the programmable features stored in its nucleobase composition and sequence, which allow it to assemble into highly advanced structures. DNA nanoassemblies are also highly controllable due to the precision of natural and artificial base-pairing, which can be manipulated by pH, temperature, metal ions, and solvent types. This programmability and molecular-level control have allowed scientists to create and utilize DNA nanostructures in one, two, and three dimensions (1D, 2D, and 3D). Initially, these 2D and 3D DNA lattices and shapes attracted a broad scientific audience because they are fundamentally captivating and structurally elegant; however, transforming these conceptual architectural blueprints into functional materials is essential for further advancements in the DNA nanotechnology field. Herein, the chemical and biological sensing applications of a 1D DNA self-assembly process known as hybridization chain reaction (HCR) are reviewed. HCR is a one-dimensional (1D) double stranded (ds) DNA assembly process initiated only in the presence of a specific short ssDNA (initiator) and two kinetically trapped DNA hairpin structures. HCR is considered an enzyme-free isothermal amplification process, which shows substantial promise and offers a wide range of applications for in situ chemical and biological sensing. Due to its modular nature, HCR can be programmed to activate only in the presence of highly specific biological and/or chemical stimuli. HCR can also be combined with different types of molecular reporters and detection approaches for various analytical readouts. While the long dsDNA HCR product may not be as structurally attractive as the 2D and 3D DNA networks, HCR is highly instrumental for applied biological, chemical, and environmental sciences, and has therefore been studied to foster a variety of objectives. In this review, we have focused on nucleic acid, protein, metabolite, and heavy metal ion detection using this 1D DNA nanotechnology via fluorescence, electrochemical, and nanoparticle-based methodologies.
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