1
|
Current molecular approach for diagnosis of MRSA: a meta-narrative review. Drug Target Insights 2022; 16:88-96. [PMID: 36761068 PMCID: PMC9906022 DOI: 10.33393/dti.2022.2522] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 12/31/2022] [Indexed: 01/19/2023] Open
Abstract
Introduction: Detection and diagnosis of methicillin-resistant Staphylococcus aureus (MRSA) are important in ensuring a correct and effective treatment, further reducing its spread. A wide range of molecular approaches has been used for the diagnosis of antimicrobial resistance (AMR) in MRSA. This review aims to study and appraise widely used molecular diagnostic methods for detecting MRSA. Methods: This meta-narrative review was performed by searching PubMed using the following search terms: (molecular diagnosis) AND (antimicrobial resistance) AND (methicillin-resistant Staphylococcus aureus). Studies using molecular diagnostic techniques for the detection of MRSA were included, while non-English language, duplicates and non-article studies were excluded. After reviewing the libraries and a further manual search, 20 studies were included in this article. RAMESES publication standard for narrative reviews was used for this synthesis. Results: A total of 20 full papers were reviewed and appraised in this synthesis, consisting of PCR technique (n = 7), deoxyribonucleic acid (DNA) Microarray (n = 1), DNA sequencing (n = 2), Xpert MRSA/SA BC assay (n = 2), matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF) (n = 2), MLST (n = 4), SCCmec typing (n = 1) and GENECUBE (n = 1). Discussion: Different diagnostic methods used to diagnose MRSA have been studied in this review. This study concludes that PCR has been extensively used due to its higher sensitivity and cost-effectiveness in the past five years
Collapse
|
2
|
Hidaka T, Nakamura M, Oritate F, Nishimura F. Comparative anaerobic digestion of sewage sludge at different temperatures with and without heat pre-treatment. CHEMOSPHERE 2022; 307:135808. [PMID: 35932923 DOI: 10.1016/j.chemosphere.2022.135808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 07/11/2022] [Accepted: 07/19/2022] [Indexed: 06/15/2023]
Abstract
Anaerobic digestion of sewage sludge is generally conducted under mesophilic (around 35 °C) or thermophilic (around 55 °C) conditions, whereas it is conducted at lower temperatures in some wastewater treatment plants without heating. In this study, we compared the anaerobic digestion of sewage sludge at 15, 25, 30, 35, 45, and 55 °C following hyperthermophilic pre-treatment at 80 °C for 24 h. Laboratory-scale reactors were operated continuously for more than 1000 days, and batch experiments were performed to evaluate the reaction kinetics. Biogas production rates at 15 °C with and without pre-treatment divided by that at 35 °C without pre-treatment were 0.73 and 0.78, respectively. The dewaterability of the digested sludge was evaluated by the capillary suction time (CST). The CST was approximately 50 s at 15 °C with and without pre-treatment and was slower than the CST at 35 °C. Compared to the shear rate, viscosity was higher at lower temperatures; however, it decreased with pre-treatment, which reduced the energy required for mixing in the reactors. Pre-treatment eliminated Escherichia coli from the sludge; however, E. coli (approximately 105 colony forming unit/g-total solids) was detected after digestion at temperatures ≤30 °C. Pre-treatment was also useful to replace a part of heat treatment required for digested sludge before it was used as fertilizer. Gene sequencing analyses indicated the effects of pre-treatment and digestion temperature on the microbial community in the digested sludge. Co-generation of biogas is useful to obtain both electricity and heat; however, heat from co-generation is sometimes limited. To maximize electricity recovery, the use of low temperature digesters has the potential to reduce fuel costs. The results indicate that anaerobic digestion at low temperatures with or without heat pre-treatment can be an efficient and cost-effective method of treating sewage sludge.
Collapse
Affiliation(s)
- Taira Hidaka
- Department of Environmental Engineering, Graduate School of Engineering, Kyoto University, Kyoto, 615-8540, Japan.
| | - Masato Nakamura
- Institute for Rural Engineering, National Agriculture and Food Research Organization, Tsukuba, 305-8609, Japan
| | - Fumiko Oritate
- Institute for Rural Engineering, National Agriculture and Food Research Organization, Tsukuba, 305-8609, Japan
| | - Fumitake Nishimura
- Research Center for Environmental Quality Management, Graduate School of Engineering, Kyoto University, Otsu, 520-0811, Japan
| |
Collapse
|
3
|
Embedding Circular Economy Principles into Urban Regeneration and Waste Management: Framework and Metrics. SUSTAINABILITY 2022. [DOI: 10.3390/su14031293] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
In a highly urbanised world, cities have become main centers of resource consumption and generation of waste. The notion of the circular economy (CE) identifies strategies for slowing and narrowing resource use through the prevention of waste, improvement of resource use, and substitution of the use of primary resources with recovered materials (and energy). The literature has recently started to explore the concept of circular cities, and a number of cities around the globe have adopted circular economy strategies. Urban regeneration can play a critical role in enabling more circular loops of resources and contribute to more sustainable urban environments; however, there is a lack of contributions in the literature that explore the circularity of urban regeneration projects. The aim of this research is to address this gap by providing a framework and metrics to embed circular economy principles into urban regeneration. The proposed framework and set of metrics are then applied to a case study in West London to quantitatively assess CE implications and point to opportunities to increase circularity. Three main scenarios are developed to assess resource impacts of different waste strategies. The maximizing recycling scenario suggests that over 65% recycling and just under 35% energy recovery could be achieved for the area. However, findings suggest potential trade-offs between strategies centered around energy recovery from waste and strategies that prioritise recycling of recyclable fractions from waste. The three scenarios are then assessed against the CE metrics proposed. Again, here, ‘maximising recycling’ better aligns with the proposed CE metrics and contributes to cutting around 50% of GHG emissions associated with management/disposal of residual waste while increasing opportunities for resource recovery. Finally, some conclusions are drawn pointing to pathways to maximise optimal resource use and infrastructural provision in urban regeneration.
Collapse
|
4
|
Varona M, Anderson JL. Advances in Mutation Detection Using Loop-Mediated Isothermal Amplification. ACS OMEGA 2021; 6:3463-3469. [PMID: 33585732 PMCID: PMC7876693 DOI: 10.1021/acsomega.0c06093] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 01/21/2021] [Indexed: 05/25/2023]
Abstract
Detection of mutations and single-nucleotide polymorphisms is highly important for diagnostic applications. Loop-mediated isothermal amplification (LAMP) is a powerful technique for the rapid and sensitive detection of nucleic acids. However, LAMP traditionally does not possess the ability to resolve single-nucleotide differences within the target sequence. Because of its speed and isothermal nature, LAMP is ideally suited for point-of-care applications in resource-limited settings. Recently, different approaches have been developed and applied to enable single-nucleotide differentiation within target sequences. This Mini-Review highlights advancements in mutation detection using LAMP. Methods involving primer design and modification to enable sequence differentiation are discussed. In addition, the development of probe-based detection methods for mutation detection are also covered.
Collapse
|
5
|
Multiplexed Diagnosis of Four Serotypes of Dengue Virus by Real-time RT-PCR. BIOCHIP JOURNAL 2020. [DOI: 10.1007/s13206-020-4409-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
|
6
|
Morinaga Y, Suzuki H, Notake S, Mizusaka T, Uemura K, Otomo S, Oi Y, Ushiki A, Kawabata N, Kameyama K, Morishita E, Uekura Y, Sugiyama A, Kawashima Y, Yanagihara K. Evaluation of GENECUBE Mycoplasma for the detection of macrolide-resistant Mycoplasma pneumoniae. J Med Microbiol 2020; 69:1346-1350. [PMID: 33141009 DOI: 10.1099/jmm.0.001264] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Introduction. Resistance against macrolide antibiotics in Mycoplasma pneumoniae is becoming non-negligible in terms of both appropriate therapy and diagnostic stewardship. Molecular methods have attractive features for the identification of Mycoplasma pneumoniae as well as its resistance-associated mutations of 23S ribosomal RNA (rRNA).Hypothesis/Gap Statement. The automated molecular diagnostic sytem can identify macrolide-resistant M. pneumoniae.Aim. To assess the performance of an automated molecular diagnostic system, GENECUBE Mycoplasma, in the detection of macrolide resistance-associated mutations.Methodology. To evaluate whether the system can distinguish mutant from wild-type 23S rRNA, synthetic oligonucleotides mimicking known mutations (high-level macrolide resistance, mutation in positions 2063 and 2064; low-level macrolide resistance, mutation in position 2067) were assayed. To evaluate clinical oropharyngeal samples, purified nucleic acids were obtained from M. pneumoniae-positive samples by using the GENECUBE system from nine hospitals. After confirmation by re-evaluation of M. pneumoniae positivity, Sanger-based sequencing of 23S rRNA and mutant typing using GENECUBE Mycoplasma were performed.Results. The system reproducibly identified all synthetic oligonucleotides associated with high-level macrolide resistance. Detection errors were only observed for A2067G (in 2 of the 10 measurements). The point mutation in 23S rRNA was detected in 67 (26.9 %) of 249 confirmed M. pneumoniae-positive clinical samples. The mutations at positions 2063, 2064 and 2617 were observed in 65 (97.0 %), 2 (3.0 %) and 0 (0.0 %) of the 67 samples, respectively. The mutations at positions 2063 and 2064 were A2063G and A2064G, respectively. The results from mutant typing using GENECUBE Mycoplasma were in full agreement with the results from sequence-based typing.Conclusion. GENECUBE Mycoplasma is a reliable test for the identification of clinically significant macrolide-resistant M. pneumoniae.
Collapse
Affiliation(s)
- Yoshitomo Morinaga
- Department of Microbiology, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, Toyama, Toyama, Japan.,Department of Laboratory Medicine, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Nagasaki, Japan
| | - Hiromichi Suzuki
- Division of Infectious Diseases, Department of Medicine, Tsukuba Medical Center Hospital, Tsukuba, Ibaraki, Japan.,Department of Clinical Laboratory Medicine, Tsukuba Medical Center Hospital, Tsukuba, Ibaraki, Japan
| | - Shigeyuki Notake
- Department of Clinical Laboratory, Tsukuba Medical Center Hospital, Tsukuba, Ibaraki, Japan
| | - Takashi Mizusaka
- Department of Clinical Laboratory, Kakogawa City Hospital, Kakogawa, Hyogo, Japan
| | - Keiichi Uemura
- Department of Clinical Laboratory, Chutoen General Medical Center, Kakegawa, Shizuoka, Japan
| | - Shinobu Otomo
- Department of Clinical Laboratory, Matsushita Memorial Hospital, Moriguchi, Osaka, Japan
| | - Yuka Oi
- Department of Clinical Laboratory, Osaka General Medical Center, Osaka, Osaka, Japan
| | - Akihito Ushiki
- Department of Clinical Laboratory, Tone-chuo-hospital, Numata, Gunma, Japan
| | - Naoki Kawabata
- Department of Clinical Laboratory, Municipal Tsuruga Hospital, Tsuruga, Fukui, Japan
| | - Kazuaki Kameyama
- Department of Clinical Laboratory, Hyogo Prefectural Kobe Children's Hospital, Kobe, Hyogo, Japan
| | - Eri Morishita
- Department of Clinical Laboratory, Akashi Medical Center, Akashi, Hyogo, Japan
| | - Yoshiko Uekura
- Tsuruga Institute of Biotechnology, TOYOBO Co., Ltd, Tsuruga, Fukui, Japan
| | - Akio Sugiyama
- Diagnostic System Department, TOYOBO Co., Ltd, Osaka, Osaka, Japan
| | - Yosuke Kawashima
- Tsuruga Institute of Biotechnology, TOYOBO Co., Ltd, Tsuruga, Fukui, Japan
| | - Katsunori Yanagihara
- Department of Laboratory Medicine, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Nagasaki, Japan
| |
Collapse
|
7
|
Biocomputing label-free security system based on homogenous ligation chain reaction-induced dramatic change in melting temperature for screening single nucleotide polymorphisms. Talanta 2020; 218:121141. [PMID: 32797898 DOI: 10.1016/j.talanta.2020.121141] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 05/03/2020] [Accepted: 05/07/2020] [Indexed: 12/17/2022]
Abstract
The development of smart platform with accurate, inexpensive and reliable detection of single-nucleotide polymorphisms (SNPs) has long been concerned in the fields of medical diagnosis and basic research. Here, we present a ligation chain reaction (LCR)-based sensing system for the cost-effective screening of SNPs by simply conducting DNA melting analysis. No chemical modification is required and the signaling operation is accomplished in homogeneous solution, circumventing the complex modification process and possibly compromised enzymatic activity associated with heterogeneous materials, such as quantum dot (QD) and gold nanoparticle (GNP). Due to the enzymatic catalysis and high fidelity of ligase, the system is capable of executing signal amplification, providing a high sensitivity and selectivity. KRAS gene is easily recognized and the site-specific mutation of guanine (G) to adenine (A), thymine (T) or cytosine (C) is accurately screened. Moreover, the excellent reliability was demonstrated by blind test and recovery test. LCR-based signaling mechanism was further used to develop the biocomputing security system, and two logic gates consisting of four single-stranded DNAs (ssDNAs) offer a double insurance to protect the information against illegal invasion, guaranteeing the reliability of output information. Once in the absence of one essential factor, the security system was always locked regardless of target key, serving as a novel strategy to ensure the safety of output information at molecular level. As a proof-of-concept scheme, this contribution introduces new insight into the development of DNA security systems and the exploitation of powerful signal transduction strategy suitable for rapid and convenient disease diagnosis.
Collapse
|
8
|
Hidaka T, Nakamura M, Oritate F, Nishimura F. Utilization of high solid waste activated sludge from small facilities by anaerobic digestion and application as fertilizer. WATER SCIENCE AND TECHNOLOGY : A JOURNAL OF THE INTERNATIONAL ASSOCIATION ON WATER POLLUTION RESEARCH 2019; 80:2320-2327. [PMID: 32245923 DOI: 10.2166/wst.2020.050] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Anaerobic co-digestion of sewage sludge with organic wastes has recently gained attention in small facilities. For small facilities, high solids sludge is suitable for transportation to a centralized co-digester, and direct utilization of the digested sludge as liquid fertilizer is recommended. Effects of high solid and hyperthermophilic pretreatment (80 °C, 24 hr) on anaerobic digestion at low temperatures and utilization as fertilizer are investigated by anaerobic/aerobic digestion and paddy soil incubation experiments. The volatile solids (VS)/total solids (TS) ratio decreases to 0.57(-), and the VS removal rate is approximately 0.7 (-) after long-term aerobic digestion. This is possibly the limitation of biodegradation, even with pretreatment, within engineering time. Substrate TS of 16% (not diluted), 10% and 5% are compared. The effect of substrate TS on biogas production performance (0.2-0.3 NL/gVS-added) is not statistically observed. Laboratory-scale paddy soil incubation experiments are performed fed with anaerobically digested pretreated or not pretreated dewatered sludge as liquid fertilizer. Pretreatment promotes nitrogen mineralization before use as fertilizer, which is helpful to prevent an outflow of surplus ammonia to the environment. The effect of soil type on microbial communities is more significant than that of anaerobically digested sludge conditions.
Collapse
Affiliation(s)
- Taira Hidaka
- Department of Environmental Engineering, Kyoto University, C1-223, Kyoto-Daigaku-Katsura, Nishikyo-ku, Kyoto, Japan E-mail:
| | - Masato Nakamura
- Institute for Rural Engineering, National Agriculture and Food Research Organization, 2-1-6, Kannondai, Tsukuba, Ibaraki, Japan
| | - Fumiko Oritate
- Headquarter, National Agriculture and Food Research Organization, 3-1-1, Kannondai, Tsukuba, Ibaraki, Japan
| | - Fumitake Nishimura
- Department of Environmental Engineering, Kyoto University, C1-223, Kyoto-Daigaku-Katsura, Nishikyo-ku, Kyoto, Japan E-mail:
| |
Collapse
|
9
|
Evaluation of performance of the GENECUBE assay for rapid molecular identification of Staphylococcus aureus and methicillin resistance in positive blood culture medium. PLoS One 2019; 14:e0219819. [PMID: 31310615 PMCID: PMC6634395 DOI: 10.1371/journal.pone.0219819] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 07/03/2019] [Indexed: 02/01/2023] Open
Abstract
Rapid identification of causative agents from positive blood culture media is a prerequisite for the timely targeted treatment of patients with sepsis. The GENECUBE (TOYOBO Co., Ltd.) is a novel, fully-automated gene analyzer that can purify DNAs and amplify target DNAs. In this study, we evaluated the ability of two newly developed GENECUBE assays to directly detect the nuc and mecA genes in blood culture medium; nuc is specific to Staphylococcus aureus, and mecA indicates methicillin resistance. We examined 263 positive blood culture samples taken at three hospitals from patients suspected of having staphylococcal bacteremia. The results were then compared with those obtained using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry, antimicrobial susceptibility testing (Microscan system or Dry-plate EIKEN), and sequencing analysis. The GENECUBE assays had sensitivity and specificity of 100% in detecting both S. aureus and methicillin resistance in positive blood culture. The turnaround time of the examination was evaluated for 36 positive blood culture samples. The time between the initiation of incubation and completion of the GENECUBE examination was 23 h (interquartile range: IQR 21–37 h); the time between reporting of Gram stain examination and completion of the GENECUBE examination was 52 min (IQR 48–62 min). These findings show that the GENECUBE assays significantly reduce the assay time with no loss of sensitivity or specificity.
Collapse
|
10
|
TANI H. Development and Application of Analytical Methods for Biological Molecules Using the Fluorescent Dyes and the Nucleotide Analogs. BUNSEKI KAGAKU 2019. [DOI: 10.2116/bunsekikagaku.68.109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
- Hidenori TANI
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology (AIST)
| |
Collapse
|
11
|
Katayama T, Yoshioka H, Yamanaka T, Takeuchi M, Muramoto Y, Usami J, Ikeda H, Sakata S. Microbial community structure in deep natural gas-bearing aquifers subjected to sulfate-containing fluid injection. J Biosci Bioeng 2018; 127:45-51. [PMID: 30082219 DOI: 10.1016/j.jbiosc.2018.06.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Revised: 06/15/2018] [Accepted: 06/18/2018] [Indexed: 10/28/2022]
Abstract
In the natural gas field located in central Japan, high concentrations of natural gases and iodide ions are dissolved in formation water and commercially produced in deep aquifers. In the iodine recovery process, the produced formation water is amended with sulfate, and this fluid is injected into gas-bearing aquifers, which may lead to infrastructure corrosion by hydrogen sulfide. In this study, we examined the microbial community in aquifers subjected to sulfate-containing fluid injection. Formation water samples were collected from production wells located at different distances from the injection wells. The chemical analysis showed that the injection fluid contained oxygen, nitrate, nitrite and sulfate, in contrast to the formation water, which had previously been shown to be depleted in these components. Sulfur isotopic analysis indicated that sulfate derived from the injection fluid was present in the sample collected from near the injection wells. Quantitative and sequencing analysis of dissimilatory sulfite reductase and 16S rRNA genes revealed that sulfate-reducing bacteria (SRB), sulfur-oxidizing bacteria, and anaerobic methanotrophic archaea (ANME) in the wells located near injection wells were more abundant than those in wells located far from the injection wells, suggesting that fluid injection stimulated these microorganisms through the addition of oxygen, nitrate, nitrite and sulfate to the methane-rich aquifers. The predominant taxa were assigned to the ANME-2 group, its sulfate-reducing partner SEEP-SRB1 cluster and sulfur-oxidizing Epsilonproteobacteria. These results provide important insights for future studies to support the development of natural gas and iodine resources in Japan.
Collapse
Affiliation(s)
- Taiki Katayama
- Institute for Geo-Resources and Environment, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki 305-8567, Japan
| | - Hideyoshi Yoshioka
- Institute for Geo-Resources and Environment, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki 305-8567, Japan.
| | - Toshiro Yamanaka
- Graduate School of Natural Science and Technology, Okayama University, 3-1-1 Tsushima-Naka, Kita-ku, Okayama 700-8530, Japan
| | - Mio Takeuchi
- Institute for Geo-Resources and Environment, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki 305-8567, Japan
| | - Yoshiyuki Muramoto
- Kanto Natural Gas Development Co., Ltd., 661 Mobara, Mobara City, Chiba 297-8550, Japan
| | - Jun Usami
- Kanto Natural Gas Development Co., Ltd., 661 Mobara, Mobara City, Chiba 297-8550, Japan
| | - Hidefumi Ikeda
- Kanto Natural Gas Development Co., Ltd., 661 Mobara, Mobara City, Chiba 297-8550, Japan
| | - Susumu Sakata
- Institute for Geo-Resources and Environment, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki 305-8567, Japan
| |
Collapse
|
12
|
Shirato K, Semba S, El-Kafrawy SA, Hassan AM, Tolah AM, Takayama I, Kageyama T, Notomi T, Kamitani W, Matsuyama S, Azhar EI. Development of fluorescent reverse transcription loop-mediated isothermal amplification (RT-LAMP) using quenching probes for the detection of the Middle East respiratory syndrome coronavirus. J Virol Methods 2018; 258:41-48. [PMID: 29763640 PMCID: PMC7113683 DOI: 10.1016/j.jviromet.2018.05.006] [Citation(s) in RCA: 83] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 04/09/2018] [Accepted: 05/10/2018] [Indexed: 11/24/2022]
Abstract
Fluorescent RT-LAMP assays using quenching probes for MERS-CoV were developed. Quenching probe (QProbe) can solve the problem in turbidity monitoring mechanism. Only primer-derived signal can be monitored specifically by QProbes. Two primer sets were developed to enable to confirm MERS case by RT-LAMP only. Both sets were highly specific and sensitive in comparison with real-time RT-PCR.
Clinical detection of Middle East respiratory syndrome (MERS) coronavirus (MERS-CoV) in patients is achieved using genetic diagnostic methods, such as real-time RT-PCR assay. Previously, we developed a reverse transcription-loop-mediated isothermal amplification (RT-LAMP) assay for the detection of MERS-CoV [Virol J. 2014. 11:139]. Generally, amplification of RT-LAMP is monitored by the turbidity induced by precipitation of magnesium pyrophosphate with newly synthesized DNA. However, this mechanism cannot completely exclude the possibility of unexpected reactions. Therefore, in this study, fluorescent RT-LAMP assays using quenching probes (QProbes) were developed specifically to monitor only primer-derived signals. Two primer sets (targeting nucleocapsid and ORF1a sequences) were constructed to confirm MERS cases by RT-LAMP assay only. Our data indicate that both primer sets were capable of detecting MERS-CoV RNA to the same level as existing genetic diagnostic methods, and that both were highly specific with no cross-reactivity observed with other respiratory viruses. These primer sets were highly efficient in amplifying target sequences derived from different MERS-CoV strains, including camel MERS-CoV. In addition, the detection efficacy of QProbe RT-LAMP was comparable to that of real-time RT-PCR assay using clinical specimens from patients in Saudi Arabia. Altogether, these results indicate that QProbe RT-LAMP assays described here can be used as powerful diagnostic tools for rapid detection and surveillance of MERS-CoV infections.
Collapse
Affiliation(s)
- Kazuya Shirato
- Laboratory of Acute Respiratory Viral Diseases and Cytokines, Department of Virology III, National Institute of Infectious Disease, 4-7-1 Gakuen, Musashimurayama, Tokyo 208-0011, Japan.
| | - Shohei Semba
- Eiken Chemical Co., Ltd., 4-19-9 Taito, Taito-ku, Tokyo 110-8408, Japan
| | - Sherif A El-Kafrawy
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Ahmed M Hassan
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Ahmed M Tolah
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Ikuyo Takayama
- Influenza virus Research Center, National Institute of Infectious Disease, 4-7-1 Gakuen, Musashimurayama, Tokyo 208-0011, Japan
| | - Tsutomu Kageyama
- Influenza virus Research Center, National Institute of Infectious Disease, 4-7-1 Gakuen, Musashimurayama, Tokyo 208-0011, Japan
| | - Tsugunori Notomi
- Eiken Chemical Co., Ltd., 4-19-9 Taito, Taito-ku, Tokyo 110-8408, Japan
| | - Wataru Kamitani
- Laboratory of Clinical Research on Infectious Diseases, Department of Pathogen Molecular Biology, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Shutoku Matsuyama
- Laboratory of Acute Respiratory Viral Diseases and Cytokines, Department of Virology III, National Institute of Infectious Disease, 4-7-1 Gakuen, Musashimurayama, Tokyo 208-0011, Japan
| | - Esam Ibraheem Azhar
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21589, Saudi Arabia; Medical Laboratory Technology Department, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| |
Collapse
|
13
|
Hidaka T, Tsushima I, Tsumori J. Comparative analyses of microbial structures and gene copy numbers in the anaerobic digestion of various types of sewage sludge. BIORESOURCE TECHNOLOGY 2018; 253:315-322. [PMID: 29367157 DOI: 10.1016/j.biortech.2017.12.097] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 12/25/2017] [Accepted: 12/27/2017] [Indexed: 06/07/2023]
Abstract
Anaerobic co-digestion of various sewage sludges is a promising approach for greater recovery of energy, but the process is more complicated than mono-digestion of sewage sludge. The applicability of microbial structure analyses and gene quantification to understand microbial conditions was evaluated. The results show that information from gene analyses is useful in managing anaerobic co-digestion and damaged microbes in addition to conventional parameters like total solids, pH and biogas production. Total bacterial 16S rRNA gene copy numbers are the most useful tools for evaluating unstable anaerobic digestion of sewage sludge, rather than mcrA and total archaeal 16S rRNA gene copy numbers, and high-throughput sequencing. First order decay rates of gene copy numbers during pH failure were higher than typical decay rates of microbes in stable operation. The sequencing analyses, including multidimensional scaling, showed very different microbial structure shifts, but the results were not consistent.
Collapse
Affiliation(s)
- Taira Hidaka
- Materials and Resources Research Group, Public Works Research Institute, 1-6, Minamihara, Tsukuba, Ibaraki 305-8516, Japan.
| | - Ikuo Tsushima
- Water Environment Research Group, Public Works Research Institute, 1-6, Minamihara, Tsukuba, Ibaraki 305-8516, Japan
| | - Jun Tsumori
- Materials and Resources Research Group, Public Works Research Institute, 1-6, Minamihara, Tsukuba, Ibaraki 305-8516, Japan
| |
Collapse
|
14
|
Ikeda K, Kasuga M, Hosoi T, Yoshii M, Sugiyama M, Wako A, Ozawa K. [Implementation and Evaluation of Genetic Testing Seminars about Lifestyle-related Disease Prevention in Pharmacy Insurance-The Need for Cooperation between the Pharmacy and the University in Genetic Testing]. YAKUGAKU ZASSHI 2017; 137:1517-1531. [PMID: 29199260 DOI: 10.1248/yakushi.16-00243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A seminar titled "Implementation and evaluation of genetic testing of lifestyle-related disease genes" was held for pharmacists, medical clerks, and clerks of pharmacy insurance, with the aim of holding seminars led by pharmacists for the general public (including patients) in the future. The subject of the seminar was single nucleotide polymorphisms in obesity-related genes and alcohol metabolism-related genes. The purpose of the seminar was to contribute to the prevention of lifestyle-related diseases of the general public. We evaluated it by administering a questionnaire to the participants before and after the seminar. After the seminar, 55% of pharmacists answered that they would like to or would strongly like to participate in genetic testing (for lifestyle-related diseases and drug metabolism-related genes) of the general public. However, some participants did not wish to do so. A customer satisfaction (CS) analysis found that this was mainly because they did not want to know the results of genetic testing of others, which they felt should be private. Most (82%) of the pharmacists answered that assistance and advice was "very necessary" or "necessary" in the participation of genetic testing. These findings show that collaboration between pharmacies and universities will be important for future seminars to the general public.
Collapse
Affiliation(s)
- Kayo Ikeda
- Department of Pharmacotherapy, Graduate School of Biomedical and Health Sciences, Hiroshima University
| | | | - Toru Hosoi
- Department of Pharmacotherapy, Graduate School of Biomedical and Health Sciences, Hiroshima University
| | - Michiko Yoshii
- Department of Pharmacotherapy, Graduate School of Biomedical and Health Sciences, Hiroshima University
| | - Masanori Sugiyama
- Department of Probiotic Science for Preventive Medicine, Graduate School of Biomedical and Health Sciences, Hiroshima University
| | | | - Koichiro Ozawa
- Department of Pharmacotherapy, Graduate School of Biomedical and Health Sciences, Hiroshima University
| |
Collapse
|
15
|
Ayukawa Y, Hanyuda S, Fujita N, Komatsu K, Arie T. Novel loop-mediated isothermal amplification (LAMP) assay with a universal QProbe can detect SNPs determining races in plant pathogenic fungi. Sci Rep 2017; 7:4253. [PMID: 28652587 PMCID: PMC5484703 DOI: 10.1038/s41598-017-04084-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Accepted: 05/09/2017] [Indexed: 12/13/2022] Open
Abstract
Tomato wilt pathogen Fusarium oxysporum f. sp. lycopersici (Fol) is grouped into three races based on their pathogenicity to different host cultivars. Rapid detection and discrimination of Fol races in field soils is important to prevent tomato wilt disease. Although five types of point mutations in secreted in xylem 3 (SIX3) gene, which are characteristic of race 3, have been reported as a molecular marker for the race, detection of these point mutations is laborious. The aim of this study is to develop a rapid and accurate method for the detection of point mutations in SIX3 of Fol. Loop-mediated isothermal amplification (LAMP) of SIX3 gene with the universal QProbe as well as two joint DNAs followed by annealing curve analysis allowed us to specifically detect Fol and discriminate race 3 among other races in about one hour. Our developed method is applicable for detection of races of other plant pathogenic fungi as well as their pesticide-resistant mutants that arise through point mutations in a particular gene.
Collapse
Affiliation(s)
- Yu Ayukawa
- United Graduate School of Agricultural Science, Tokyo University of Agriculture and Technology (TUAT), Fuchu, Tokyo, 183-8509, Japan
- Laboratory of Plant Pathology, Graduate School of Agriculture, Tokyo University of Agriculture and Technology (TUAT), Fuchu, Tokyo, 183-8509, Japan
| | - Saeri Hanyuda
- Laboratory of Plant Pathology, Graduate School of Agriculture, Tokyo University of Agriculture and Technology (TUAT), Fuchu, Tokyo, 183-8509, Japan
| | - Naoko Fujita
- Laboratory of Plant Pathology, Graduate School of Agriculture, Tokyo University of Agriculture and Technology (TUAT), Fuchu, Tokyo, 183-8509, Japan
| | - Ken Komatsu
- United Graduate School of Agricultural Science, Tokyo University of Agriculture and Technology (TUAT), Fuchu, Tokyo, 183-8509, Japan.
- Laboratory of Plant Pathology, Graduate School of Agriculture, Tokyo University of Agriculture and Technology (TUAT), Fuchu, Tokyo, 183-8509, Japan.
| | - Tsutomu Arie
- United Graduate School of Agricultural Science, Tokyo University of Agriculture and Technology (TUAT), Fuchu, Tokyo, 183-8509, Japan
- Laboratory of Plant Pathology, Graduate School of Agriculture, Tokyo University of Agriculture and Technology (TUAT), Fuchu, Tokyo, 183-8509, Japan
| |
Collapse
|
16
|
Yasmeen A, Du F, Zhao Y, Dong J, Chen H, Huang X, Cui X, Tang Z. Sequence-Specific Biosensing of DNA Target through Relay PCR with Small-Molecule Fluorophore. ACS Chem Biol 2016; 11:1945-51. [PMID: 27158915 DOI: 10.1021/acschembio.5b01081] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Polymerase chain reaction coupled with signal generation offers sensitive recognition of target DNA sequence; however, these procedures require fluorophore-labeled oligonucleotide probes and high-tech equipment to achieve high specificity. Therefore, intensive research has been conducted to develop reliable, convenient, and economical DNA detection methods. The relay PCR described here is the first sequence-specific detection method using a small-molecule fluorophore as a sensor and combines the classic 5'-3' exonuclease activity of Taq polymerase with an RNA mimic of GFP to build a label-free DNA detection platform. Primarily, Taq polymerase cleaves the 5' noncomplementary overhang of the target specific probe during extension of the leading primer to release a relay oligo to initiate tandem PCR of the reporting template, which encodes the sequence of RNA aptamer. Afterward, the PCR product is transcribed to mRNA, which could generate a fluorescent signal in the presence of corresponding fluorophore. In addition to high sensitivity and specificity, the flexibility of choosing different fluorescent reporting signals makes this method versatile in either single or multiple target detection.
Collapse
Affiliation(s)
- Afshan Yasmeen
- Natural
Products Research Center, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, People’s Republic of China
| | - Feng Du
- Natural
Products Research Center, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, People’s Republic of China
| | - Yongyun Zhao
- Natural
Products Research Center, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, People’s Republic of China
| | - Juan Dong
- Natural
Products Research Center, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, People’s Republic of China
| | - Haodong Chen
- Natural
Products Research Center, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, People’s Republic of China
| | - Xin Huang
- Natural
Products Research Center, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, People’s Republic of China
| | - Xin Cui
- Natural
Products Research Center, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, People’s Republic of China
| | - Zhuo Tang
- Natural
Products Research Center, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, People’s Republic of China
| |
Collapse
|
17
|
Katayama T, Yoshioka H, Takahashi HA, Amo M, Fujii T, Sakata S. Changes in microbial communities associated with gas hydrates in subseafloor sediments from the Nankai Trough. FEMS Microbiol Ecol 2016; 92:fiw093. [DOI: 10.1093/femsec/fiw093] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/30/2016] [Indexed: 01/17/2023] Open
|
18
|
Ikeda K, Hosoi T, Yoshii M, Sugiyama M, Ozawa K. [Implementation and Evaluation of Genetic Testing Seminars on Lifestyle-related Disease Prevention for Pharmacy Students]. YAKUGAKU ZASSHI 2016; 136:337-50. [PMID: 26831811 DOI: 10.1248/yakushi.15-00170] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The field of pharmacotherapy has advanced to use molecular targeted agents, and pharmacists are now encouraged to focus on pharmacogenomics. A seminar titled "Implementation and evaluation of genetic testing of lifestyle-related disease genes" was presented to students at the Faculty of Pharmaceutical Sciences, Hiroshima University, describing the pharmacogenomic role of single nucleotide polymorphisms in obesity-related genes and alcohol metabolism-related genes. The seminar topic was selected first because pharmaceutical students were already familiar with some of the content, and secondly because we believe that pharmacists should be informed about the prevention of lifestyle-related diseases using genetic testing. We evaluated the usefulness of this seminar by administering a questionnaire before and after the seminar to participating students. Several points requiring improvement were identified, although 82% of students stated that the seminar was "very useful" or "useful". We conclude that this educational seminar was useful to students of pharmaceutical sciences.
Collapse
Affiliation(s)
- Kayo Ikeda
- Department of Pharmacotherapy, Graduate School of Biomedical and Health Sciences, Hiroshima University
| | | | | | | | | |
Collapse
|
19
|
Morishita S, Takahashi K, Araki M, Hironaka Y, Sunami Y, Edahiro Y, Tsutsui M, Ohsaka A, Tsuneda S, Komatsu N. Melting curve analysis after T allele enrichment (MelcaTle) as a highly sensitive and reliable method for detecting the JAK2V617F mutation. PLoS One 2015; 10:e0122003. [PMID: 25794279 PMCID: PMC4368779 DOI: 10.1371/journal.pone.0122003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2014] [Accepted: 02/11/2015] [Indexed: 01/23/2023] Open
Abstract
Detection of the JAK2V617F mutation is essential for diagnosing patients with classical myeloproliferative neoplasms (MPNs). However, detection of the low-frequency JAK2V617F mutation is a challenging task due to the necessity of discriminating between true-positive and false-positive results. Here, we have developed a highly sensitive and accurate assay for the detection of JAK2V617F and named it melting curve analysis after T allele enrichment (MelcaTle). MelcaTle comprises three steps: 1) two cycles of JAK2V617F allele enrichment by PCR amplification followed by BsaXI digestion, 2) selective amplification of the JAK2V617F allele in the presence of a bridged nucleic acid (BNA) probe, and 3) a melting curve assay using a BODIPY-FL-labeled oligonucleotide. Using this assay, we successfully detected nearly a single copy of the JAK2V617F allele, without false-positive signals, using 10 ng of genomic DNA standard. Furthermore, MelcaTle showed no positive signals in 90 assays screening healthy individuals for JAK2V617F. When applying MelcaTle to 27 patients who were initially classified as JAK2V617F-positive on the basis of allele-specific PCR analysis and were thus suspected as having MPNs, we found that two of the patients were actually JAK2V617F-negative. A more careful clinical data analysis revealed that these two patients had developed transient erythrocytosis of unknown etiology but not polycythemia vera, a subtype of MPNs. These findings indicate that the newly developed MelcaTle assay should markedly improve the diagnosis of JAK2V617F-positive MPNs.
Collapse
Affiliation(s)
- Soji Morishita
- Department of Transfusion Medicine and Stem Cell Regulation, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Kochi Takahashi
- Department of Life Science and Medical Bioscience, Waseda University, Tokyo, Japan
- Department of Hematology, Juntendo University School of Medicine, Tokyo, Japan
| | - Marito Araki
- Department of Transfusion Medicine and Stem Cell Regulation, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Yumi Hironaka
- Department of Hematology, Juntendo University School of Medicine, Tokyo, Japan
| | - Yoshitaka Sunami
- Department of Hematology, Juntendo University School of Medicine, Tokyo, Japan
| | - Yoko Edahiro
- Department of Hematology, Juntendo University School of Medicine, Tokyo, Japan
| | - Miyuki Tsutsui
- Department of Hematology, Juntendo University School of Medicine, Tokyo, Japan
| | - Akimichi Ohsaka
- Department of Transfusion Medicine and Stem Cell Regulation, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Satoshi Tsuneda
- Department of Life Science and Medical Bioscience, Waseda University, Tokyo, Japan
| | - Norio Komatsu
- Department of Hematology, Juntendo University School of Medicine, Tokyo, Japan
- * E-mail:
| |
Collapse
|
20
|
|
21
|
Tamura T, Katsuda N, Hamajima N. A PCR method for VKORC1 G-1639A and CYP2C9 A1075C genotyping useful to warfarin therapy among Japanese. SPRINGERPLUS 2014; 3:499. [PMID: 25932358 PMCID: PMC4409611 DOI: 10.1186/2193-1801-3-499] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Accepted: 08/27/2014] [Indexed: 01/08/2023]
Abstract
Warfarin is widely prescribed for patients with the risk of thromboembolism around the world. The inter-individual and inter-racial differences in appropriate dosage depend highly on age, body weight, and genetic factors. A lot of studies including genome-wide association studies revealed that vitamin K epoxide reductase complex, subunit 1 (VKORC1) G-1639A and Cytochrome P450 (CYP) 2C9 A1075C are the most strong genetic factors for determining warfarin effects in Asians and Africans. Since we developed a quick and inexpensive genotyping method, polymerase chain reaction with confronting two-pair primers (PCR-CTPP), the method was applied for these genotypes to examine the possibility to clinical use. Subjects were 436 examinees (117 males and 319 females, aged 32 to 85 years) who attended a health checkup program in Japan. The PCR-CTPP for VKORC1 G-1639A and CYP2C9 A1075C was conducted for the subjects, as well as the samples genotyped by DigiTag2 method. The allele frequencies of VKORC1 G-1639A were 0.085 for G and 0.915 for A, and those of CYP2C9 A1075C were 0.979 for A and 0.021 for C, being in Hardy-Weinberg equilibrium (p = 0.658 and p = 0.514, respectively). These frequencies were similar to those reported in the HapMap project. Genotyping for both SNPs by PCR-CTPP was replicated by DigiTag2 method. Our results indicated that the PCR-CTPP could be one of the alternative methods for genotyping VKORC1 G-1639A and CYP2C9 A1075C for Asians and Africans with similar allele frequencies to Japanese.
Collapse
Affiliation(s)
- Takashi Tamura
- Department of Epidemiology and Preventive Medicine, Gifu University Graduate School of Medicine, 1-1 Yanagido, Gifu, 501-1194 Japan
| | | | - Nobuyuki Hamajima
- Department of Healthcare Administration, Nagoya University Graduate School of Medicine, Nagoya, Japan
| |
Collapse
|
22
|
Faltin B, Zengerle R, von Stetten F. Current methods for fluorescence-based universal sequence-dependent detection of nucleic acids in homogenous assays and clinical applications. Clin Chem 2013; 59:1567-82. [PMID: 23938456 DOI: 10.1373/clinchem.2013.205211] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
BACKGROUND Specific and sensitive nucleic acid (NA) testing in research and clinical diagnostics is usually performed by use of labeled oligonucleotide probes. However, the use of target-specific fluorogenic probes increases the cost of analysis. Therefore, universal sequence-dependent (USD) NA detection methods have been developed to facilitate cost-effective target detection using standardized reagents. CONTENT We provide a comprehensive review of the current methods for fluorescence-based USD NA detection. Initially, we focus on the emergence of these methods as a means to overcome the shortcomings of common NA detection methods, such as hydrolysis probes and molecular beacons. Thereafter, we provide a critical evaluation of the individual detection methods. These methods include (a) target amplification with bipartite primers introducing a universal detection tag to the amplicon (UniPrimer PCR, universal fluorescence energy transfer probe PCR, attached universal duplex probe PCR, and universal strand displacement amplification) or combined with bipartite probes comprising a universal detection region (mediator probe PCR, universal strand displacement amplification, universal quenching probe PCR) and (b) amplification-independent assays employing either a universal variant of the invader assay or universal NA hybridization sensors. We discuss differences between the methods and review clinical applications. SUMMARY The current methods for USD NA testing are cost-effective and flexible and have concordant analytical performance in comparison with common probe-based techniques. They can detect any target sequence by the simple use of a label-free, low-cost primer or probe combined with a universal fluorogenic reporter. The methods differ in the number of target specificities, capability of multiplexing, and incubation requirements (isothermal/thermocycling). Extensive clinical applications comprise detection of single-nucleotide polymorphisms, study of gene expression, in situ PCR, and quantification of pathogen load.
Collapse
|
23
|
Niu S, Lou X, Jiang Y, Lin J. A Novel Fluorescence Sensor for Cocaine with Signal Amplification through Cycling Exo-Cleaving with a Hairpin Probe. ANAL LETT 2012. [DOI: 10.1080/00032719.2012.677972] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
|
24
|
Faltin B, Wadle S, Roth G, Zengerle R, von Stetten F. Mediator probe PCR: a novel approach for detection of real-time PCR based on label-free primary probes and standardized secondary universal fluorogenic reporters. Clin Chem 2012; 58:1546-56. [PMID: 22923452 DOI: 10.1373/clinchem.2012.186734] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
BACKGROUND The majority of established techniques for monitoring real-time PCR amplification involve individual target-specific fluorogenic probes. For analysis of numerous different targets the synthesis of these probes contributes to the overall cost during assay development. Sequence-dependent universal detection techniques overcome this drawback but are prone to detection of unspecific amplification products. We developed the mediator probe PCR as a solution to these problems. METHODS A set of label-free sequence-specific primary probes (mediator probes), each comprising a target-specific region and a standardized mediator tag, is cleaved upon annealing to its target sequence by the polymerases' 5' nuclease activity. Release of a mediator triggers signal generation by cleavage of a complementary fluorogenic reporter probe. RESULTS Real-time PCR amplification of human papillomavirus 18 (HPV18), Staphylococcus aureus, Escherichia coli, and Homo sapiens DNA dilution series showed exceptional linearity when detected either by novel mediator probes (r(2) = 0.991-0.999) or state-of-the-art hydrolysis probes (TaqMan probes) (r(2) = 0.975-0.993). For amplification of HPV18 DNA the limits of detection were 78.3 and 85.1 copies per 10-μL reaction when analyzed with the mediator probe and hydrolysis probe, respectively. Duplex amplification of HPV18 target DNA and internal standard had no effects on back calculation of target copy numbers when quantified with either the mediator probe PCR (r(2) = 0.998) or the hydrolysis probe PCR (r(2) = 0.988). CONCLUSIONS The mediator probe PCR has equal performance to hydrolysis probe PCR and has reduced costs because of the use of universal fluorogenic reporters.
Collapse
Affiliation(s)
- Bernd Faltin
- Laboratory for MEMS Applications, Department of Microsystems Engineering-IMTEK, University of Freiburg, Freiburg, Germany
| | | | | | | | | |
Collapse
|
25
|
Kouguchi Y, Yamaji M, Kuramoto M, Shimatani M. Sequence-specific detection using a universal probe system based on the formation of a four-way junction structure. Anal Biochem 2011; 408:332-6. [DOI: 10.1016/j.ab.2010.09.036] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2010] [Revised: 09/24/2010] [Accepted: 09/24/2010] [Indexed: 10/19/2022]
|
26
|
Nepomnyashchii AB, Cho S, Rossky PJ, Bard AJ. Dependence of electrochemical and electrogenerated chemiluminescence properties on the structure of BODIPY dyes. Unusually large separation between sequential electron transfers. J Am Chem Soc 2010; 132:17550-9. [PMID: 21090724 DOI: 10.1021/ja108108d] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Electrochemistry and electrogenerated chemiluminescence (ECL) of selected substituted BODIPY (4,4-difluoro-4-bora-3a,4a-diaza-s-indacene) dyes have been studied. The location and nature of substituents on positions 1-8 are important in predicting the behavior, and especially the stability, of the radical ions formed on electron transfer. Dyes with unsubstituted positions 2, 6, and 8 show a kinetic contribution to both oxidation and reduction. Dyes with only unsubstituted positions 2 and 6 and a substituted 8 position show chemically reversible reduction but irreversible oxidation. Unsubstituted positions 2 and 6 tend to show dimer formation on oxidation. Completely substituted dyes show nernstian oxidation and reduction. Oxidation and reduction studies of simple BODIPY dyes show an unusually large separation between the first and second reduction peaks and also the first and second oxidation peaks, of about 1.1 V, which is very different from that observed for polycyclic hydrocarbons and other heteroaromatic compounds, where the spacing is usually about 0.5 V. Electronic structure calculations confirmed this behavior, and this effect is attributed to a greater electronic energy required to withdraw or add a second electron and a lower relative solvation energy for the dianion or dication compared with those of the polycyclic hydrocarbons. ECL was generated for all compounds either by annihilation or by using a co-reactant.
Collapse
Affiliation(s)
- Alexander B Nepomnyashchii
- Center for Electrochemistry and Chemistry and Biochemistry Department, The University of Texas at Austin, Austin, Texas 78712, USA
| | | | | | | |
Collapse
|