1
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Goyal S, Singh P, Sengupta S, Muthukrishnan AB, Jayaraman G. DNA-Aptamer-Based qPCR Using Light-Up Dyes for the Detection of Nucleic Acids. ACS OMEGA 2023; 8:47277-47282. [PMID: 38107963 PMCID: PMC10719997 DOI: 10.1021/acsomega.3c07599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Revised: 11/05/2023] [Accepted: 11/16/2023] [Indexed: 12/19/2023]
Abstract
Quantitative polymerase chain reaction (qPCR) is widely used in detection of nucleic acids, but existing methods either lack sequence-specific detection or are costly because they use chemically modified DNA probes. In this work, we apply a DNA aptamer and light-up dye-based chemistry for qPCR for nucleic acid quantification. In contrast to the conventional qPCR, in our method, we observe an exponential decrease in fluorescence upon DNA amplification. The qPCR method we developed produced consistent Ct vs log10 (DNA amount) standard curves, which have a linearfit with R2 value > 0.99. This qPCR technique was validated by quantifying gene targets from Streptococcus zooepidemicus (SzhasB) and Mycobacterium tuberculosis (MtrpoB). We show that our strategy is able to successfully detect DNA at as low as 800 copies/μL. To the best of our knowledge, this is the first study demonstrating the application of light-up dyes and DNA aptamers in qPCR.
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Affiliation(s)
| | - Prashant Singh
- Department of Biotechnology,
Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, Tamil Nadu 600036, India
| | - Sudeshna Sengupta
- Department of Biotechnology,
Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, Tamil Nadu 600036, India
| | - Anantha Barathi Muthukrishnan
- Department of Biotechnology,
Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, Tamil Nadu 600036, India
| | - Guhan Jayaraman
- Department of Biotechnology,
Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, Tamil Nadu 600036, India
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2
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Zheng Y, Li X, Deng S, Zhao H, Ye Y, Zhang S, Huang X, Bai R, Zhuang L, Zhou Q, Li M, Su J, Li R, Bao X, Zeng L, Chen R, Zheng J, Lin D, He C, Zhang J, Zuo Z. CSTF2 mediated mRNA N 6-methyladenosine modification drives pancreatic ductal adenocarcinoma m 6A subtypes. Nat Commun 2023; 14:6334. [PMID: 37816727 PMCID: PMC10564946 DOI: 10.1038/s41467-023-41861-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 09/21/2023] [Indexed: 10/12/2023] Open
Abstract
N6-methyladenosine (m6A) modification of gene transcripts plays critical roles in cancer. Here we report transcriptomic m6A profiling in 98 tissue samples from 65 individuals with pancreatic ductal adenocarcinoma (PDAC). We identify 17,996 m6A peaks with 195 hyper-methylated and 93 hypo-methylated in PDAC compared with adjacent normal tissues. The differential m6A modifications distinguish two PDAC subtypes with different prognosis outcomes. The formation of the two subtypes is driven by a newly identified m6A regulator CSTF2 that co-transcriptionally regulates m6A installation through slowing the RNA Pol II elongation rate during gene transcription. We find that most of the CSTF2-regulated m6As have positive effects on the RNA level of host genes, and CSTF2-regulated m6As are mainly recognized by IGF2BP2, an m6A reader that stabilizes mRNAs. These results provide a promising PDAC subtyping strategy and potential therapeutic targets for precision medicine of PDAC.
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Affiliation(s)
- Yanfen Zheng
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Xingyang Li
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Shuang Deng
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Hongzhe Zhao
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Ying Ye
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Shaoping Zhang
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Xudong Huang
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Ruihong Bai
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Lisha Zhuang
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Quanbo Zhou
- Department of Pancreaticobiliary Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Mei Li
- Department of Pathology, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Jiachun Su
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Rui Li
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Xiaoqiong Bao
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Lingxing Zeng
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Rufu Chen
- Guangdong Provincial People's Hospital & Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Jian Zheng
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, Nanjing Medical University, Nanjing, China
- Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, China
| | - Dongxin Lin
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China.
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, Nanjing Medical University, Nanjing, China.
- Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
| | - Chuan He
- Department of Chemistry, The University of Chicago, Chicago, IL, USA.
- Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA.
- Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA.
| | - Jialiang Zhang
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China.
| | - Zhixiang Zuo
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China.
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3
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Molecular Epidemiology of Begomoviruses Infecting Mungbean from Yellow Mosaic Disease Hotspot Regions of India. Appl Biochem Biotechnol 2023:10.1007/s12010-023-04402-3. [PMID: 36853442 DOI: 10.1007/s12010-023-04402-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/17/2023] [Indexed: 03/01/2023]
Abstract
The major threat to mungbean (Vigna radiata L.) cultivation in the Indian subcontinent is yellow mosaic diseases (YMD), caused by Begomovirus containing bipartite genomes (DNA-A and DNA-B). In the current study, we address the epidemiology of begomoviruses infecting mungbean plants in three YMD hotspot regions of India. Full-length genomic components of the viruses from the symptomatic leaves were cloned by rolling circle amplification (RCA) and sequenced. Mungbean yellow mosaic virus (MYMV) was detected in Bihar and mungbean yellow mosaic India virus (MYMIV) in Assam and Orissa. Furthermore, we studied the population structure and genetic diversity of MYMV and MYMIV isolates of Vigna species reported to date from India. Interestingly, based on phylogenetics, we observed independent evolution of DNA-A and coevolution of DNA-B of MYMV and MYMIV. This finding is supported by the high mutation rate and recombination events in DNA-B, particularly in BV1 and BC1 genes over DNA-A, with high transition/transversion bias (R) for DNA-A over DNA-B. To investigate the effect of Begomovirus infection in plants, we constructed infectious clones (i.e. MYMV and MYMIV) and inoculated them to eight mungbean genotypes, cowpea (Vigna unguiculata L.) and tobacco (Nicotiana benthamiana) through agroinfiltration. The infected plants developed varying degrees of typical YMD symptoms. Based on the disease severity score and viral titre, mungbean genotypes were categorized as highly susceptible to MYMV (ML267) and MYMIV (K851) and immune to MYMV (PDM139, SML668) and MYMIV (Pusa Vishal). Conclusively, our findings may help prevent an epidemic of YMD in Vigna species and develop mungbean genotypes resistant to YMD via breeding programs.
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4
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Loop mediated isothermal amplification for detection of foodborne parasites: A journey from lab to lab-on-a-chip. Food Control 2022. [DOI: 10.1016/j.foodcont.2022.109251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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5
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ATXN2-mediated translation of TNFR1 promotes esophageal squamous cell carcinoma via m 6A-dependent manner. Mol Ther 2022; 30:1089-1103. [PMID: 34995801 PMCID: PMC8899599 DOI: 10.1016/j.ymthe.2022.01.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 11/02/2021] [Accepted: 01/03/2022] [Indexed: 12/12/2022] Open
Abstract
N6-methyladenosine (m6A) is the most prevalent RNA modification, and the effect of its dysregulation on esophageal squamous cell carcinoma (ESCC) development remains unclear. Here, by performing transcriptome-wide m6A sequencing in 16 ESCC tissue samples, we identified the key roles of m6A in TNFRSF1A (also known as TNFR1)-mediated MAPK and NF-κB activation in ESCC. Mechanistically, a functional protein involved in m6A methylation, ATXN2, is identified that augments the translation of TNFRSF1A by binding to m6A-modified TNFRSF1A mRNA. Upregulation of the TNFRSF1A protein level, a vital upstream switch for TNFRSF1A-mediated signaling events, activates the NF-κB and MAPK pathways and thus promotes ESCC development. Furthermore, TNFRSF1A m6A modifications and protein levels are upregulated in ESCC, and high levels of TNFRSF1A m6A and protein are correlated with poor ESCC patient survival. These results collectively indicate that the m6A-TNFRSF1A axis is critical for ESCC development and thus may serve as a potential druggable target.
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Pearson LA, D'Agostino PM, Neilan BA. Recent developments in quantitative PCR for monitoring harmful marine microalgae. HARMFUL ALGAE 2021; 108:102096. [PMID: 34588118 DOI: 10.1016/j.hal.2021.102096] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 08/17/2021] [Accepted: 08/19/2021] [Indexed: 06/13/2023]
Abstract
Marine microalgae produce a variety of specialised metabolites that have toxic effects on humans, farmed fish, and marine wildlife. Alarmingly, many of these compounds bioaccumulate in the tissues of shellfish and higher trophic organisms, including species consumed by humans. Molecular methods are emerging as a potential alternative and complement to the conventional microscopic diagnosis of toxic or otherwise harmful microalgal species. Quantitative PCR (qPCR) in particular, has gained popularity over the past decade as a sensitive, rapid, and cost-effective method for monitoring harmful microalgae. Assays targeting taxonomic marker genes provide the opportunity to identify and quantify (or semi-quantify) microalgal species and importantly to pre-empt bloom events. Moreover, the discovery of paralytic shellfish toxin biosynthesis genes in dinoflagellates has enabled researchers to directly monitor toxigenic species in coastal waters and fisheries. This review summarises the recent developments in qPCR detection methods for harmful microalgae, with emphasis on emerging toxin gene monitoring technologies.
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Affiliation(s)
- Leanne A Pearson
- School of Environmental and Life Sciences, The University of Newcastle, Callaghan, NSW, 2308, Australia
| | - Paul M D'Agostino
- Chair of Technical Biochemistry, Technical University of Dresden, Dresden, Germany
| | - Brett A Neilan
- School of Environmental and Life Sciences, The University of Newcastle, Callaghan, NSW, 2308, Australia.
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Alhamlan FS, Al-Qahtani AA, Bakheet DM, Bohol MF, Althawadi SI, Mutabagani MS, Almaghrabi RS, Obeid DA. Development and validation of an in-house, low-cost SARS-CoV-2 detection assay. J Infect Public Health 2021; 14:1139-1143. [PMID: 34343964 PMCID: PMC8280604 DOI: 10.1016/j.jiph.2021.07.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 03/15/2021] [Accepted: 07/13/2021] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND One major challenge for detecting the virus that causes COVID-19 is commercial SARS-CoV-2 testing kit or reagent availability. To allow every laboratory or hospital access to an in-house assay, we developed a low-cost SARS-CoV-2 detection assay protocol using in-house primers and reagents/equipment on hand in most biology or diagnostic laboratories: a SYBR Green-based RT-PCR. RNA extraction has also become a major bottleneck due to limited supplies and the required labor. Thus, we validated an alternative RNA extraction protocol. METHODS We designed and synthesized in-house primers according to SARS-CoV-2 genome sequences retrieved from GISAID database. One hundred and ninety patient samples were collected by nasopharyngeal swab, coded, and used to develop and validate the assay protocol. RNA extraction was performed using TRI reagent-based RNA protocol to inactivate the virus; thus, testing was conducted in a conventional biosafety level 2 laboratory. RESULTS The sensitivity and specificity of the primers were evaluated using 190 patient samples previously tested for SARS-CoV-2. The positive amplicons were sequenced to confirm the results. The assay protocol was developed, and the specificity of each RT-PCR product was confirmed using melting curve analyses. Of 190 samples, the SYBR Green-based RT-PCR assay detected SARS-CoV-2 target genes in 88 samples, with no false-positive results. These findings indicate that the sensitivity of our assay was 97.7% and specificity of 100% with those of the diagnostic laboratory that tested the same samples using a Rotor-Gene PCR cycler with an Altona Diagnostics SARS-CoV-2 kit (R2 = 0.89). CONCLUSIONS These approaches are reliable, repeatable, specific, sensitive, simple, and low-cost tools for the detection of SARS-CoV-2 in a conventional biosafety level 2 laboratory, offering alternative approaches when commercial kits are unavailable or not affordable.
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Affiliation(s)
- Fatimah S Alhamlan
- Department of Infection and Immunity, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia; College of Medicine, Alfaisal University, Riyadh, Saudi Arabia; Department of Pathology and Laboratory Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia.
| | - Ahmed A Al-Qahtani
- Department of Infection and Immunity, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia; College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | - Dana M Bakheet
- College of Medicine, Alfaisal University, Riyadh, Saudi Arabia; Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Marie F Bohol
- Department of Infection and Immunity, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Sahar I Althawadi
- Department of Pathology and Laboratory Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Maysoon S Mutabagani
- Department of Pathology and Laboratory Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Reem S Almaghrabi
- Department of Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Dalia A Obeid
- Department of Infection and Immunity, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
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8
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Furuse T, Mizuma H, Hirose Y, Kushida T, Yamada I, Miura I, Masuya H, Funato H, Yanagisawa M, Onoe H, Wakana S. A new mouse model of GLUT1 deficiency syndrome exhibits abnormal sleep-wake patterns and alterations of glucose kinetics in the brain. Dis Model Mech 2019; 12:dmm.038828. [PMID: 31399478 PMCID: PMC6765196 DOI: 10.1242/dmm.038828] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Accepted: 07/30/2019] [Indexed: 11/29/2022] Open
Abstract
Dysfunction of glucose transporter 1 (GLUT1) proteins causes infantile epilepsy, which is designated as a GLUT1 deficiency syndrome (GLUT1DS; OMIM #606777). Patients with GLUT1DS display varied clinical phenotypes, such as infantile seizures, ataxia, severe mental retardation with learning disabilities, delayed development, hypoglycorrhachia, and other varied symptoms. Glut1Rgsc200 mutant mice mutagenized with N-ethyl-N-nitrosourea (ENU) carry a missense mutation in the Glut1 gene that results in amino acid substitution at the 324th residue of the GLUT1 protein. In this study, these mutants exhibited various phenotypes, including embryonic lethality of homozygotes, a decreased cerebrospinal-fluid glucose value, deficits in contextual learning, a reduction in body size, seizure-like behavior and abnormal electroencephalogram (EEG) patterns. During EEG recording, the abnormality occurred spontaneously, whereas the seizure-like phenotypes were not observed at the same time. In sleep-wake analysis using EEG recording, heterozygotes exhibited a longer duration of wake times and shorter duration of non-rapid eye movement (NREM) sleep time. The shortened period of NREM sleep and prolonged duration of the wake period may resemble the sleep disturbances commonly observed in patients with GLUT1DS and other epilepsy disorders. Interestingly, an in vivo kinetic analysis of glucose utilization by positron emission tomography with 2-deoxy-2-[fluorine-18]fluoro-D-glucose imaging revealed that glucose transportation was reduced, whereas hexokinase activity and glucose metabolism were enhanced. These results indicate that a Glut1Rgsc200 mutant is a useful tool for elucidating the molecular mechanisms of GLUT1DS. This article has an associated First Person interview with the joint first authors of the paper. Summary: New phenotypes are revealed by a GLUT1 deficiency mutant mouse model carrying a missense mutation in Glut1.
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Affiliation(s)
- Tamio Furuse
- Japan Mouse Clinic, RIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Hiroshi Mizuma
- Laboratory for Pathophysiological and Health Science, RIKEN Center for Biosystems Dynamics Research, Kobe, Hyogo 650-0047, Japan
| | - Yuuki Hirose
- International Institute for Integrative Sleep Medicine (WPI-IIIS), University of Tsukuba, Ibaraki 305-8575, Japan
| | - Tomoko Kushida
- Japan Mouse Clinic, RIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Ikuko Yamada
- Japan Mouse Clinic, RIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Ikuo Miura
- Japan Mouse Clinic, RIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Hiroshi Masuya
- Resource Advancement Unit, Integrated Bioresource Information Division, RIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Hiromasa Funato
- International Institute for Integrative Sleep Medicine (WPI-IIIS), University of Tsukuba, Ibaraki 305-8575, Japan.,Department of Anatomy, School of Medicine, Faculty of Medicine, Toho University, Tokyo 143-8540, Japan
| | - Masashi Yanagisawa
- International Institute for Integrative Sleep Medicine (WPI-IIIS), University of Tsukuba, Ibaraki 305-8575, Japan.,Life Science Center for Survival Dynamics (TARA), University of Tsukuba, Ibaraki 305-8575, Japan.,Department of Molecular Genetics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Hirotaka Onoe
- Human Brain Research Center, Kyoto University Graduate School of Medicine, Kyoto 606-8501, Japan
| | - Shigeharu Wakana
- Japan Mouse Clinic, RIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074, Japan
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Wang M, Hang J, Abuzeid AMI, Huang Y, Fu Y, Yan X, Zhang P, Huo C, Liu Y, Ran R, Sun Y, Li G. Development of multi-ARMS-qPCR method for detection of hookworms from cats and dogs. Parasitol Int 2019; 73:101974. [PMID: 31421266 DOI: 10.1016/j.parint.2019.101974] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2018] [Revised: 08/06/2019] [Accepted: 08/13/2019] [Indexed: 11/17/2022]
Abstract
Hookworms are blood-sucking nematodes that infect dogs, cats, and humans, causing iron-deficiency anemia, abdominal pain, diarrhea, and skin inflammation. Amplification refractory mutation system (ARMS) is a modified technology based on allele-specific PCR, which is widely used in mutation detection and genotyping. However, no data about ARMS application in hookworm detection. This study aims to establish a multi-ARMS-qPCR method for the detection of three hookworm species from dogs and cats. A universal forward primer and three specific primers (ARMS-Cey, ARMS-Can, and ARMS-Tub) were designed based on the three ITS SNPs (ITS250, ITS78 and ITS153) of Ancylostoma ceylanicum, A. caninum, and A. tubaeforme, respectively. The results showed that the three designed ARMS primers generated specific melting curves for the three hookworms' standard plasmids. The melting temperature (Tm) values were 88.40 °C (A. ceylanicum), 83.15 °C (A. caninum), and 85.65 °C (A. tubaeforme), with good reproducibility of intra- and inter-assay. No amplification was observed with other intestinal parasites. The limit of detection using the established technique was 1, 2, and 104 egg per gram feces (EPG) for A. caninum, A. tubaeforme and A. ceylanicum, respectively. Using multi-ARMS-qPCR assay, 17 out of 50 fecal samples were positive for hookworms, including ten single and seven mixed infections, and single infections were quantified. In conclusion, the used multi-ARMS-qPCR method has the advantages of high efficiency, sensitivity, specificity, and quantitative analysis and can be used for the clinical detection, epidemiological investigation, and zoonotic risk assessment of canine and feline hookworms.
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Affiliation(s)
- Mingwei Wang
- Guangdong Provincial Zoonosis Prevention and Control Key Laboratory, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510542, China
| | - Jianxiong Hang
- Guangdong Provincial Zoonosis Prevention and Control Key Laboratory, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510542, China
| | - Asmaa M I Abuzeid
- Guangdong Provincial Zoonosis Prevention and Control Key Laboratory, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510542, China
| | - Yue Huang
- Guangdong Provincial Zoonosis Prevention and Control Key Laboratory, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510542, China
| | - Yeqi Fu
- Guangdong Provincial Zoonosis Prevention and Control Key Laboratory, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510542, China
| | - Xinxin Yan
- Guangdong Provincial Zoonosis Prevention and Control Key Laboratory, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510542, China
| | - Pan Zhang
- Guangdong Provincial Zoonosis Prevention and Control Key Laboratory, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510542, China
| | - Chenyang Huo
- Guangdong Provincial Zoonosis Prevention and Control Key Laboratory, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510542, China
| | - Yunqiu Liu
- Guangdong Provincial Zoonosis Prevention and Control Key Laboratory, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510542, China
| | - Rongkun Ran
- Guangdong Provincial Zoonosis Prevention and Control Key Laboratory, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510542, China
| | - Yongxiang Sun
- Guangdong Provincial Zoonosis Prevention and Control Key Laboratory, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510542, China
| | - Guoqing Li
- Guangdong Provincial Zoonosis Prevention and Control Key Laboratory, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510542, China.
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10
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Yi C, Hong Y. Estimating the Copy Number of Transgenes in Transformed Cotton by Real-Time Quantitative PCR. Methods Mol Biol 2019; 1902:137-157. [PMID: 30543067 DOI: 10.1007/978-1-4939-8952-2_11] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Transgenic cotton has been widely employed both in commercial cultivation and basic research. It is essential to determine which plants contain the transgene and in how many copies after transgenic cotton plants are generated. A TaqMan quantitative real-time polymerase chain reaction (Tq RT-PCR) method is described here to examine transgene copy number in transgenic cotton plants. The estimation of two transgene elements, the target gene of green fluorescence protein (GFP) and the selective gene of neomycin phosphotransferase II (NPTII), is used as an example to detail each step in Tq RT-PCR procedure, including endogenous reference gene selection, reference plasmid construction, primer-probe design, DNA extraction, real-time PCR, and data analysis. Comparing with traditional Southern hybridization analysis, this method can be used efficiently in screening large number of seedlings of T0 transgenic cotton at early stage of transformation process as well as in identifying transgene homozygotes in a segregation population.
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Affiliation(s)
- Chengxin Yi
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
- JOil (S) Pte Ltd, Singapore, Singapore
| | - Yan Hong
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.
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11
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Zhang J, Bai R, Li M, Ye H, Wu C, Wang C, Li S, Tan L, Mai D, Li G, Pan L, Zheng Y, Su J, Ye Y, Fu Z, Zheng S, Zuo Z, Liu Z, Zhao Q, Che X, Xie D, Jia W, Zeng MS, Tan W, Chen R, Xu RH, Zheng J, Lin D. Excessive miR-25-3p maturation via N 6-methyladenosine stimulated by cigarette smoke promotes pancreatic cancer progression. Nat Commun 2019; 10:1858. [PMID: 31015415 PMCID: PMC6478927 DOI: 10.1038/s41467-019-09712-x] [Citation(s) in RCA: 231] [Impact Index Per Article: 46.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Accepted: 03/26/2019] [Indexed: 12/15/2022] Open
Abstract
N6-methyladenosine (m6A) modification is an important mechanism in miRNA processing and maturation, but the role of its aberrant regulation in human diseases remained unclear. Here, we demonstrate that oncogenic primary microRNA-25 (miR-25) in pancreatic duct epithelial cells can be excessively maturated by cigarette smoke condensate (CSC) via enhanced m6A modification that is mediated by NF-κB associated protein (NKAP). This modification is catalyzed by overexpressed methyltransferase-like 3 (METTL3) due to hypomethylation of the METTL3 promoter also caused by CSC. Mature miR-25, miR-25-3p, suppresses PH domain leucine-rich repeat protein phosphatase 2 (PHLPP2), resulting in the activation of oncogenic AKT-p70S6K signaling, which provokes malignant phenotypes of pancreatic cancer cells. High levels of miR-25-3p are detected in smokers and in pancreatic cancers tissues that are correlated with poor prognosis of pancreatic cancer patients. These results collectively indicate that cigarette smoke-induced miR-25-3p excessive maturation via m6A modification promotes the development and progression of pancreatic cancer.
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MESH Headings
- Adenosine/analogs & derivatives
- Adenosine/metabolism
- Adult
- Aged
- Aged, 80 and over
- Carcinoma, Pancreatic Ductal/blood
- Carcinoma, Pancreatic Ductal/etiology
- Carcinoma, Pancreatic Ductal/mortality
- Carcinoma, Pancreatic Ductal/pathology
- Cell Line, Tumor
- Cell Transformation, Neoplastic/genetics
- Co-Repressor Proteins/metabolism
- DNA Methylation
- Disease Progression
- Epithelial Cells/pathology
- Female
- Follow-Up Studies
- Gene Expression Regulation, Neoplastic
- HEK293 Cells
- Humans
- Male
- Methyltransferases/genetics
- Methyltransferases/metabolism
- MicroRNAs/blood
- MicroRNAs/metabolism
- Middle Aged
- Nuclear Proteins/metabolism
- Pancreatic Ducts/cytology
- Pancreatic Ducts/pathology
- Pancreatic Neoplasms/blood
- Pancreatic Neoplasms/etiology
- Pancreatic Neoplasms/mortality
- Pancreatic Neoplasms/pathology
- Phosphoprotein Phosphatases/genetics
- Phosphoprotein Phosphatases/metabolism
- Prognosis
- Promoter Regions, Genetic/genetics
- Proto-Oncogene Proteins c-akt/metabolism
- RNA-Binding Proteins/metabolism
- Repressor Proteins
- Ribosomal Protein S6 Kinases, 70-kDa/metabolism
- Smoke/adverse effects
- Smoking/adverse effects
- Smoking/blood
- Nicotiana/toxicity
- Up-Regulation
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Affiliation(s)
- Jialiang Zhang
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China and Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Ruihong Bai
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China and Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Mei Li
- Department of Pathology, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Huilin Ye
- Department of Pancreaticobiliary Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Chen Wu
- Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- CAMS Key Laboratory of Genetics and Genomic Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Chengfeng Wang
- Department of Abdominal Surgery, National Cancer Center/National Clinical Research Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Shengping Li
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China and Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Liping Tan
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China and Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Dongmei Mai
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China and Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Guolin Li
- Department of Pancreaticobiliary Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Ling Pan
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China and Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Yanfen Zheng
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China and Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Jiachun Su
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China and Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Ying Ye
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China and Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Zhiqiang Fu
- Department of Pancreaticobiliary Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Shangyou Zheng
- Department of Pancreaticobiliary Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Zhixiang Zuo
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China and Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Zexian Liu
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China and Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Qi Zhao
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China and Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Xu Che
- Department of Abdominal Surgery, National Cancer Center/National Clinical Research Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Dan Xie
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China and Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Weihua Jia
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China and Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Mu-Sheng Zeng
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China and Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Wen Tan
- Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- CAMS Key Laboratory of Genetics and Genomic Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Rufu Chen
- Department of Pancreaticobiliary Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China.
| | - Rui-Hua Xu
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China and Collaborative Innovation Center for Cancer Medicine, Guangzhou, China.
| | - Jian Zheng
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China and Collaborative Innovation Center for Cancer Medicine, Guangzhou, China.
| | - Dongxin Lin
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China and Collaborative Innovation Center for Cancer Medicine, Guangzhou, China.
- Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
- CAMS Key Laboratory of Genetics and Genomic Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
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12
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Green MR, Sambrook J. Analysis of DNA by Agarose Gel Electrophoresis. Cold Spring Harb Protoc 2019; 2019:2019/1/pdb.top100388. [PMID: 30602561 DOI: 10.1101/pdb.top100388] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Electrophoresis through agarose or polyacrylamide gels is used to separate, analyze, identify, and purify DNA fragments. The technique is simple, rapid to perform, and capable of resolving fragments of DNA that cannot be separated adequately by other procedures, such as density gradient centrifugation. The location of bands of DNA within the gel can be determined directly by staining with low concentrations of fluorescent intercalating dyes, such as ethidium bromide or SYBR Gold; bands containing as little as 20 pg of double-stranded DNA can then be detected by direct examination of the gel in ultraviolet (UV) light. If necessary, these bands of DNA can be recovered from the gel.
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13
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14
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Srinivasan S, Ranganathan V, DeRosa MC, Murari BM. Label-free aptasensors based on fluorescent screening assays for the detection of Salmonella typhimurium. Anal Biochem 2018; 559:17-23. [PMID: 30081031 DOI: 10.1016/j.ab.2018.08.002] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 08/02/2018] [Accepted: 08/02/2018] [Indexed: 10/28/2022]
Abstract
We report two label-free fluorescent aptasensor methods for the detection of S. typhimurium. In the first method, we have used a ''turn off'' approach in which the aptamer is first intercalated with SYBR Green I (SG), leading to a greatly enhanced fluorescence signal. The addition of S. typhimurium (approximately 1530-96938 CFU/mL), which specifically binds with its aptamer and releases SG, leads to a linear decrease in fluorescence intensity. The lowest detection limit achieved with this approach was in the range of 733 CFU/mL. In the second method, a ''turn on'' approach was designed for S. typhimurium through the Förster resonance energy transfer (FRET) between Rhodamine B (RB) and gold nanoparticles (AuNPs). When the aptamer and AuNPs were mixed with RB, the fluorescence of RB was significantly quenched via FRET. The aptamer adsorbs to the AuNP surface to protect them from salt-induced aggregation, which leads to the fluorescence quenching of RB in presence of AuNPs. Upon the addition of S. typhimurium, S. typhimurium specifically binds with its aptamer and loses the capability to stabilize AuNPs. Thus, the salt easily induces the aggregation of AuNPs, resulting in the fluorescence recovery of the quenched RB. S. typhimurium concentrations ranging from 1530 to 96938 CFU/mL with the detection limit of 464 CFU/mL was achieved with this methodology. Given these data, some insights into the molecular interactions between the aptamer and the bacterial target are provided. These aptasensor methods also may be adapted for the detection of a wide variety of targets.
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Affiliation(s)
- Sathya Srinivasan
- Department of Biotechnology, School of Bioscience and Technology, VIT University, Vellore, 632 104, TN, India; Department of Chemistry, Carleton University, 1125 Colonel By Drive, Ottawa, ON K1S 5B6, Canada.
| | - Velu Ranganathan
- Department of Chemistry, Carleton University, 1125 Colonel By Drive, Ottawa, ON K1S 5B6, Canada.
| | - Maria C DeRosa
- Department of Chemistry, Carleton University, 1125 Colonel By Drive, Ottawa, ON K1S 5B6, Canada.
| | - Bhaskar Mohan Murari
- Department of Biotechnology, School of Bioscience and Technology, VIT University, Vellore, 632 104, TN, India; Department of Sensor and Biomedical Technology, School of Electronics Engineering, VIT University, Vellore, 632 104, TN, India.
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15
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Agudo R, Calvo PA, Martínez-Jiménez MI, Blanco L. Engineering human PrimPol into an efficient RNA-dependent-DNA primase/polymerase. Nucleic Acids Res 2017; 45:9046-9058. [PMID: 28911121 PMCID: PMC5587808 DOI: 10.1093/nar/gkx633] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Accepted: 07/12/2017] [Indexed: 02/01/2023] Open
Abstract
We have developed a straightforward fluorometric assay to measure primase-polymerase activity of human PrimPol (HsPrimPol). The sensitivity of this procedure uncovered a novel RNA-dependent DNA priming-polymerization activity (RdDP) of this enzyme. In an attempt to enhance HsPrimPol RdDP activity, we constructed a smart mutant library guided by prior sequence-function analysis, and tested this library in an adapted screening platform of our fluorometric assay. After screening less than 500 variants, we found a specific HsPrimPol mutant, Y89R, which displays 10-fold higher RdDP activity than the wild-type enzyme. The improvement of RdDP activity in the Y89R variant was due mainly to an increased in the stabilization of the preternary complex (protein:template:incoming nucleotide), a specific step preceding dimer formation. Finally, in support of the biotechnological potential of PrimPol as a DNA primer maker during reverse transcription, mutant Y89R HsPrimPol rendered up to 17-fold more DNA than with random hexamer primers.
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Affiliation(s)
- Rubén Agudo
- Centro de Biología Molecular ‘Severo Ochoa’ (CSIC-UAM), Cantoblanco, E-28049 Madrid, Spain
- To whom correspondence should be addressed. Tel: +34 91 196 46 85; Fax: +34 91 196 44 20; . Correspondence may also be addressed to Rubén Agudo. Tel: +34 91 196 46 86; Fax: +34 91 196 44 20;
| | - Patricia A. Calvo
- Centro de Biología Molecular ‘Severo Ochoa’ (CSIC-UAM), Cantoblanco, E-28049 Madrid, Spain
| | | | - Luis Blanco
- Centro de Biología Molecular ‘Severo Ochoa’ (CSIC-UAM), Cantoblanco, E-28049 Madrid, Spain
- To whom correspondence should be addressed. Tel: +34 91 196 46 85; Fax: +34 91 196 44 20; . Correspondence may also be addressed to Rubén Agudo. Tel: +34 91 196 46 86; Fax: +34 91 196 44 20;
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16
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Kappel A, Keller A. miRNA assays in the clinical laboratory: workflow, detection technologies and automation aspects. Clin Chem Lab Med 2017; 55:636-647. [PMID: 27987355 DOI: 10.1515/cclm-2016-0467] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 11/01/2016] [Indexed: 12/27/2022]
Abstract
microRNAs (miRNAs) are short non-coding RNA molecules that regulate gene expression in eukaryotes. Their differential abundance is indicative or even causative for a variety of pathological processes including cancer or cardiovascular disorders. Due to their important biological function, miRNAs represent a promising class of novel biomarkers that may be used to diagnose life-threatening diseases, and to monitor disease progression. Further, they may guide treatment selection or dosage of drugs. miRNAs from blood or derived fractions are particularly interesting candidates for routine laboratory applications, as they can be measured in most clinical laboratories already today. This assures a good accessibility of respective tests. Albeit their great potential, miRNA-based diagnostic tests have not made their way yet into the clinical routine, and hence no standardized workflows have been established to measure miRNAs for patients' benefit. In this review we summarize the detection technologies and workflow options that exist to measure miRNAs, and we describe the advantages and disadvantages of each of these options. Moreover, we also provide a perspective on data analysis aspects that are vital for translation of raw data into actionable diagnostic test results.
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Affiliation(s)
- Andreas Kappel
- Siemens Healthcare GmbH, Guenther-Scharowsky-Str.1, Erlangen
| | - Andreas Keller
- Chair for Clinical Bioinformatics, Saarland University, University Hospital, Saarbruecken
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17
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Li Y, Liu N, Liu H, Wang Y, Hao Y, Ma X, Li X, Huo Y, Lu J, Tang S, Wang C, Zhang Y, Gao Z. A novel label-free fluorescence assay for one-step sensitive detection of Hg 2+ in environmental drinking water samples. Sci Rep 2017; 7:45974. [PMID: 28378768 PMCID: PMC5380999 DOI: 10.1038/srep45974] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Accepted: 03/07/2017] [Indexed: 01/11/2023] Open
Abstract
A novel label-free fluorescence assay for detection of Hg2+ was developed based on the Hg2+-binding single-stranded DNA (ssDNA) and SYBR Green I (SG I). Differences from other assays, the designed rich-thymine (T) ssDNA probe without fluorescent labelling can be rapidly formed a T-Hg2+-T complex and folded into a stable hairpin structure in the presence of Hg2+ in environmental drinking water samples by facilitating fluorescence increase through intercalating with SG I in one-step. In the assay, the fluorescence signal can be directly obtained without additional incubation within 1 min. The dynamic quantitative working ranges was 5–1000 nM, the determination coefficients were satisfied by optimization of the reaction conditions. The lowest detection limit of Hg2+ was 3 nM which is well below the standard of U.S. Environmental Protection Agency. This method was highly specific for detecting of Hg2+ without being affected by other possible interfering ions from different background compositions of water samples. The recoveries of Hg2+ spiked in these samples were 95.05–103.51%. The proposed method is more viable, low-costing and simple for operation in field detection than the other methods with great potentials, such as emergency disposal, environmental monitoring, surveillance and supporting of ecological risk assessment and management.
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Affiliation(s)
- Ya Li
- School of Public Health, Lanzhou University, Lanzhou 73000, P. R. China.,Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Health and Environmental Medicine, Tianjin, 300050, P. R. China
| | - Nan Liu
- School of Public Health, Lanzhou University, Lanzhou 73000, P. R. China.,Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Health and Environmental Medicine, Tianjin, 300050, P. R. China.,School of Public Health, State Ministry of Education, Sun Yat-sen University, Guangzhou, Guangdong, 510080, P. R. China.,Department of Nutrition and Food Hygiene, College of Public Health, Zhengzhou University, Zhengzhou, 450001, P. R. China
| | - Hui Liu
- School of Public Health, Lanzhou University, Lanzhou 73000, P. R. China
| | - Yu Wang
- School of Public Health, Lanzhou University, Lanzhou 73000, P. R. China
| | - Yuwei Hao
- School of Public Health, Lanzhou University, Lanzhou 73000, P. R. China
| | - Xinhua Ma
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Health and Environmental Medicine, Tianjin, 300050, P. R. China
| | - Xiaoli Li
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Health and Environmental Medicine, Tianjin, 300050, P. R. China
| | - Yapeng Huo
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Health and Environmental Medicine, Tianjin, 300050, P. R. China
| | - Jiahai Lu
- School of Public Health, State Ministry of Education, Sun Yat-sen University, Guangzhou, Guangdong, 510080, P. R. China
| | - Shuge Tang
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Health and Environmental Medicine, Tianjin, 300050, P. R. China.,Department of Nutrition and Food Hygiene, College of Public Health, Zhengzhou University, Zhengzhou, 450001, P. R. China
| | - Caiqin Wang
- School of Public Health, Lanzhou University, Lanzhou 73000, P. R. China.,Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Health and Environmental Medicine, Tianjin, 300050, P. R. China
| | - Yinhong Zhang
- School of Public Health, Lanzhou University, Lanzhou 73000, P. R. China
| | - Zhixian Gao
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Health and Environmental Medicine, Tianjin, 300050, P. R. China
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18
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Sequence specific sorting of DNA molecules with FACS using 3dPCR. Sci Rep 2017; 7:39385. [PMID: 28051104 PMCID: PMC5209659 DOI: 10.1038/srep39385] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Accepted: 11/22/2016] [Indexed: 12/04/2022] Open
Abstract
Genetic heterogeneity is an important feature of many biological systems, but introduces technical challenges to their characterization. Even with the best modern instruments, only a small fraction of DNA molecules present in a sample can be read, and they are recovered in the form of short, hundred-base reads. In this paper, we introduce 3dPCR, a method to sort DNA molecules with sequence specificity. 3dPCR allows heterogeneous populations of DNA to be sorted to recover long targets for deep sequencing. It is valuable whenever a target sequence is rare in a mixed population, such as for characterizing mutations in heterogeneous cancer cell populations or identifying cells containing a specific genetic sequence or infected with a target virus.
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19
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Huang D, Yan G, Gudmestad N, Skantar A. Quantification of Paratrichodorus allius in DNA extracted from soil using TaqMan Probe and SYBR Green real-time PCR assays. NEMATOLOGY 2017. [DOI: 10.1163/15685411-00003101] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The ectoparasitic stubby root nematode,Paratrichodorus allius, transmits tobacco rattle virus, which causes corky ringspot disease resulting in significant economic losses in the potato industry. A diagnostic method for direct quantification ofP. alliusfrom soil DNA using TaqMan probe and SYBR Green real-time PCR assays was developed to assist the potato industry in management of this important vector. Specificity of primers/probe designed from the internal transcribed spacer of ribosomal DNA ofP. alliuswas demonstrated byin silicoanalysis and experimental PCR tests with no cross reactions using non-target nematode species and nematode communities. The SYBR Green method was more sensitive than the TaqMan probe method during detection using serial diluted DNA templates. Standard curves were generated from serial dilutions of DNA extracted from autoclaved soil with artificially inoculatedP. alliusindividuals and were validated by high correlations between the numbers of target nematodes quantified by the assays and added to the soil. Moreover, the numbers ofP. alliusdetermined by the real-time PCR assays and estimated by the microscopic method in 17 field soil samples presented positive correlation relationships (). Although the quantification using TaqMan probe overestimated the target nematodes compared to using SYBR Green in eight out of ten field soil samples, results of the two methods correlated well (). This is the first report ofP. alliusquantification from soil DNA extracts using real-time PCR, providing a rapid and sensitive diagnostic method obviating time-consuming manual nematode extraction from soil and microscopic identification and quantification.
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Affiliation(s)
- Danqiong Huang
- North Dakota State University, Department of Plant Pathology, Walster Hall 306, Fargo, ND 58102, USA
| | - Guiping Yan
- North Dakota State University, Department of Plant Pathology, Walster Hall 306, Fargo, ND 58102, USA
| | - Neil Gudmestad
- North Dakota State University, Department of Plant Pathology, Walster Hall 306, Fargo, ND 58102, USA
| | - Andrea Skantar
- USDA-ARS, Mycology and Nematology Genetic Diversity and Biology Laboratory, 10300 Baltimore Avenue, Building 010A, RM. 238, Barc-West, Beltsville, MD 20705, USA
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20
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Chovelon B, Fiore E, Faure P, Peyrin E, Ravelet C. A lifetime-sensitive fluorescence anisotropy probe for DNA-based bioassays: The case of SYBR Green. Biosens Bioelectron 2016; 90:140-145. [PMID: 27886600 DOI: 10.1016/j.bios.2016.11.049] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Revised: 09/01/2016] [Accepted: 11/20/2016] [Indexed: 12/12/2022]
Abstract
In standard steady-state fluorescence anisotropy (FA) DNA-based assays, the ligand binding to a given receptor is typically signalled by the rotational correlation time changes of the tracer. Herein, we report a radically different strategy that relies on the peculiar excited state lifetime features of the SYBR Green (SG) dye. This DNA-binding probe exhibits a drastically short lifetime in solution, leading to a high FA signal. Its complexation to oligonucleotides determines a singular and very large depolarization depending on the concerted effects of extreme lifetime enhancement and resonance energy homotransfer. On the basis of ligand-induced changes in the molar fractions of bound and free forms of SG, the approach provides an unprecedented means for the FA monitoring of the ligand binding to short DNA molecules, allowing the elaboration of a variety of intercalator displacement assays and label-free biosensors that involve diverse DNA structures (duplex, hairpin, G-quadruplex and single-stranded), ligand types (ion, small organic molecule and protein) and binding modes (intercalation, minor groove, allosteric switch). These findings open up promising avenues in the design of a new generation of FA assays.
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Affiliation(s)
- Benoit Chovelon
- University Grenoble Alpes, DPM UMR 5063, F-38041 Grenoble, France; CNRS, DPM UMR 5063, F-38041 Grenoble, France; Département de Biochimie, Toxicologie et Pharmacologie, CHU de Grenoble site Nord - Institut de biologie et de pathologie, F-38041 Grenoble, France
| | - Emmanuelle Fiore
- University Grenoble Alpes, DPM UMR 5063, F-38041 Grenoble, France; CNRS, DPM UMR 5063, F-38041 Grenoble, France
| | - Patrice Faure
- Département de Biochimie, Toxicologie et Pharmacologie, CHU de Grenoble site Nord - Institut de biologie et de pathologie, F-38041 Grenoble, France; University Grenoble Alpes, Laboratory of Hypoxy Physiopathology Study Inserm U1042, 38700 La Tronche, France
| | - Eric Peyrin
- University Grenoble Alpes, DPM UMR 5063, F-38041 Grenoble, France; CNRS, DPM UMR 5063, F-38041 Grenoble, France.
| | - Corinne Ravelet
- University Grenoble Alpes, DPM UMR 5063, F-38041 Grenoble, France; CNRS, DPM UMR 5063, F-38041 Grenoble, France.
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21
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Sumii K, Miyake H, Enatsu N, Chiba K, Fujisawa M. Characterization of urocortin as an anti-apoptotic protein in experimental ischemia-reperfusion model of the rat testis. Biochem Biophys Res Commun 2016; 479:387-392. [PMID: 27659706 DOI: 10.1016/j.bbrc.2016.09.091] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 09/19/2016] [Indexed: 12/26/2022]
Abstract
The objective of this study was to investigate the role of urocortin in testicular apoptosis using an experimental ischemia-reperfusion rat model. To evaluate the change in urocortin expression and apoptotic status in the testes following ischemia-reperfusion, the left testes of rats were rotated clockwise by 720° for 1 h, and were then harvested at 0, 1, 3, 6 and 24 h after detorsion (n = 5 in each group). A time-dependent increase in the expression levels of urocortin was noted until 6 h after reperfusion, but the expression of urocortin was markedly decreased 24 h after reperfusion. However, a TUNEL assay showed that the proportion of germ cells undergoing apoptosis significantly increased 24 h after reperfusion compared with that of 6 h after reperfusion. To clarify whether or not urocortin directly regulates the testicular apoptosis induced by ischemia-reperfusion, either astressin, an antagonist of urocortin, or normal saline was injected into the rat testes 15 min before detorsion, followed by the testicular torsion. The testes were then removed 3 h after detorsion (n = 5 in each group). The testicular injection of astressin significantly increased the proportion of TUNEL-positive germ cells, and significantly decreased expression of Bcl-2 and Bcl-xL. In addition, the level of phosphorylated ERK 1/2, but not that of phosphorylated Akt, was significantly reduced by the intratesticular administration of astressin. These findings suggest that urocortin may play a cytoprotective role in the germ cells in response to ischemia-reperfusion injury through the activation of major anti-apoptotic proteins, as well as by the mitogen-activated protein kinase signaling pathway activation.
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Affiliation(s)
- Kenta Sumii
- Division of Urology, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe 650-0017, Japan.
| | - Hideaki Miyake
- Department of Urology, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu 431-3192, Japan
| | - Noritoshi Enatsu
- Division of Urology, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe 650-0017, Japan
| | - Koji Chiba
- Division of Urology, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe 650-0017, Japan
| | - Masato Fujisawa
- Division of Urology, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe 650-0017, Japan
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22
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Frossard A, Hammes F, Gessner MO. Flow Cytometric Assessment of Bacterial Abundance in Soils, Sediments and Sludge. Front Microbiol 2016; 7:903. [PMID: 27379043 PMCID: PMC4905975 DOI: 10.3389/fmicb.2016.00903] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Accepted: 05/26/2016] [Indexed: 11/13/2022] Open
Abstract
Bacterial abundance is a fundamental measure in microbiology, but its assessment is often tedious, especially for soil, and sediment samples. To overcome this limitation, we adopted a time-efficient flow-cytometric (FCM) counting method involving cell detachment and separation from matrix particles by centrifugation in tubes receiving sample suspensions and Histodenz® solution. We used this approach to assess bacterial abundances in diverse soils (natural and agricultural), sediments (streams and lakes) and sludge from sand-filters in a drinking water treatment plant and compared the results to bacterial abundances determined by two established methods, epifluorescence microscopy (EM) and adenosine triphosphate (ATP) quantification. Cell abundances determined by FCM and EM correlated fairly well, although absolute cell abundances were generally lower when determined by FCM. FCM also showed significant relations with cell counts converted from ATP concentrations, although estimates derived from ATP determinations were typically higher, indicating the presence of ATP sources other than bacteria. Soil and sediment organic matter (OM) content influenced the goodness of fit between counts obtained with EM and FCM. In particular, bacterial abundance determined by FCM in samples containing less than 10% OM, such as stream sediment, was particularly well correlated with the cell counts assessed by EM. Overall, these results suggest that FCM following cell detachment and purification is a useful approach to increase sample throughput for determining bacterial abundances in soils, sediments and sludge. However, notable scatter and only partial concordance among the FCM and reference methods suggests that protocols require further improvement for assessments requiring high precision, especially when OM contents in samples are high.
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Affiliation(s)
- Aline Frossard
- Forest Soils and Biogeochemistry, Swiss Federal Institute for Forest, Snow and Landscape Research (WSL)Birmensdorf Switzerland; Department of Aquatic Ecology, Swiss Federal Institute of Aquatic Science and Technology (Eawag)Dübendorf Switzerland; Department of Experimental Limnology, Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), StechlinGermany; Institute of Integrative Biology (IBZ), ETH ZürichZürich Switzerland
| | - Frederik Hammes
- Department of Environmental Microbiology, Swiss Federal Institute of Aquatic Science and Technology (Eawag) Dübendorf Switzerland
| | - Mark O Gessner
- Department of Aquatic Ecology, Swiss Federal Institute of Aquatic Science and Technology (Eawag)Dübendorf Switzerland; Department of Experimental Limnology, Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), StechlinGermany; Institute of Integrative Biology (IBZ), ETH ZürichZürich Switzerland; Department of Ecology, Berlin Institute of Technology (TU Berlin)Berlin Germany
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Pancreatic cancer risk variant in LINC00673 creates a miR-1231 binding site and interferes with PTPN11 degradation. Nat Genet 2016; 48:747-57. [DOI: 10.1038/ng.3568] [Citation(s) in RCA: 202] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Accepted: 04/15/2016] [Indexed: 02/07/2023]
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24
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Guo Y, Xu L, Hong S, Sun Q, Yao W, Pei R. Label-free DNA-based biosensors using structure-selective light-up dyes. Analyst 2016; 141:6481-6489. [DOI: 10.1039/c6an01958g] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Label-free biosensors (LFBs) have demonstrated great potential in cost-effective applications. This review collected the latest reported works which employed structure-selective nucleic acid dyes for the development of DNA-based LFBs.
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Affiliation(s)
- Yahui Guo
- State Key Laboratory of Food Science and Technology
- School of Food Science and Technology
- Jiangnan University
- Wuxi 214122
- China
| | - Lijun Xu
- Key Laboratory of Nano-Bio Interface
- Division of Nanobiomedicine
- Suzhou Institute of Nano-Tech and Nano-Bionics
- Chinese Academy of Sciences
- Suzhou 215123
| | - Shanni Hong
- Key Laboratory of Nano-Bio Interface
- Division of Nanobiomedicine
- Suzhou Institute of Nano-Tech and Nano-Bionics
- Chinese Academy of Sciences
- Suzhou 215123
| | - Qingqing Sun
- State Key Laboratory of Food Science and Technology
- School of Food Science and Technology
- Jiangnan University
- Wuxi 214122
- China
| | - Weirong Yao
- State Key Laboratory of Food Science and Technology
- School of Food Science and Technology
- Jiangnan University
- Wuxi 214122
- China
| | - Renjun Pei
- Key Laboratory of Nano-Bio Interface
- Division of Nanobiomedicine
- Suzhou Institute of Nano-Tech and Nano-Bionics
- Chinese Academy of Sciences
- Suzhou 215123
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25
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Candesartan Mediated Amelioration of Cisplatin-Induced Testicular Damage Is Associated with Alterations in Expression Patterns of Nephrin and Podocin. BIOMED RESEARCH INTERNATIONAL 2015; 2015:273784. [PMID: 26539476 PMCID: PMC4619786 DOI: 10.1155/2015/273784] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Accepted: 07/30/2015] [Indexed: 11/18/2022]
Abstract
Nephrin and podocin are known to be closely related to the pharmacological effects of angiotensin-II receptor blocker (ARB). The objectives of this study were to investigate the role of nephrin and podocin using cisplatin-induced testicular damage and to evaluate the effect of ARB. At first, we evaluated the effects of cisplatin either alone or in combination with ARB candesartan on changes in expression patterns of nephrin and podocin in the rat testes. We then conducted in vitro studies to investigate the effects of angiotensin using cultured Sertoli cells, line TM4. As a result, the expression of nephrin and podocin was shown to localize around the basal membrane of seminiferous tubules. Treatment with cisplatin resulted in a marked decrease in the expression of nephrin and podocin and induced a shift of both proteins from linear to granular expression patterns, accompanying the increased apoptotic index in the testes; these changes were partially restored by the additional administration of candesartan. In vitro studies with TM4 revealed the angiotensin-II mediated expression changes of nephrin and podocin. These findings suggest that candesartan can prevent cisplatin-induced testicular damage by regulating expression patterns of the nephrin-podocin complex in the testes.
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26
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Noris E, Miozzi L. Real-time PCR protocols for the quantification of the begomovirus tomato yellow leaf curl Sardinia virus in tomato plants and in its insect vector. Methods Mol Biol 2015; 1236:61-72. [PMID: 25287496 DOI: 10.1007/978-1-4939-1743-3_6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Tomato yellow leaf curl Sardinia virus (TYLCSV) (Geminiviridae) is an important pathogen, transmitted by the whitefly Bemisia tabaci, that severely affects the tomato production in the Mediterranean basin. Here, we describe real-time PCR protocols suitable for relative and absolute quantification of TYLCSV in tomato plants and in whitefly extracts. Using primers and probe specifically designed for TYLCSV, the protocols for relative quantification allow to compare the amount of TYLCSV present in different plant or whitefly samples, normalized to the amount of DNA present in each sample using endogenous tomato or Bemisia genes as internal references. The absolute quantification protocol allows to calculate the number of genomic units of TYLCSV over the genomic units of the plant host (tomato), with a sensitivity of as few as ten viral genome copies per sample. The described protocols are potentially suitable for several applications, such as plant breeding for resistance, analysis of virus replication, and virus-vector interaction studies.
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Affiliation(s)
- Emanuela Noris
- Institute for Sustainable Plant Protection (IPSP), National Research Council (CNR), Strada delle Cacce 73, 10135, Torino, Italy,
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27
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González TI, Espina M, Sierra LM, Bettmer J, Blanco-González E, Montes-Bayón M, Sanz-Medel A. Enhanced Detection of DNA Sequences Using End-Point PCR Amplification and Online Gel Electrophoresis (GE)-ICP-MS: Determination of Gene Copy Number Variations. Anal Chem 2014; 86:11028-32. [DOI: 10.1021/ac502671f] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- T. Iglesias González
- Department of Physical and Analytical
Chemistry, Faculty of Chemistry, ‡Department of Functional
Biology (Genetic Area) and Oncology University Institute (IUOPA), University of Oviedo, C/Julian Clavería 8, 33006 Oviedo, Spain
| | - M. Espina
- Department of Physical and Analytical
Chemistry, Faculty of Chemistry, ‡Department of Functional
Biology (Genetic Area) and Oncology University Institute (IUOPA), University of Oviedo, C/Julian Clavería 8, 33006 Oviedo, Spain
| | - L. M. Sierra
- Department of Physical and Analytical
Chemistry, Faculty of Chemistry, ‡Department of Functional
Biology (Genetic Area) and Oncology University Institute (IUOPA), University of Oviedo, C/Julian Clavería 8, 33006 Oviedo, Spain
| | - J. Bettmer
- Department of Physical and Analytical
Chemistry, Faculty of Chemistry, ‡Department of Functional
Biology (Genetic Area) and Oncology University Institute (IUOPA), University of Oviedo, C/Julian Clavería 8, 33006 Oviedo, Spain
| | - E. Blanco-González
- Department of Physical and Analytical
Chemistry, Faculty of Chemistry, ‡Department of Functional
Biology (Genetic Area) and Oncology University Institute (IUOPA), University of Oviedo, C/Julian Clavería 8, 33006 Oviedo, Spain
| | - M. Montes-Bayón
- Department of Physical and Analytical
Chemistry, Faculty of Chemistry, ‡Department of Functional
Biology (Genetic Area) and Oncology University Institute (IUOPA), University of Oviedo, C/Julian Clavería 8, 33006 Oviedo, Spain
| | - A. Sanz-Medel
- Department of Physical and Analytical
Chemistry, Faculty of Chemistry, ‡Department of Functional
Biology (Genetic Area) and Oncology University Institute (IUOPA), University of Oviedo, C/Julian Clavería 8, 33006 Oviedo, Spain
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Hardikar AA, Farr RJ, Joglekar MV. Circulating microRNAs: understanding the limits for quantitative measurement by real-time PCR. J Am Heart Assoc 2014; 3:e000792. [PMID: 24572259 PMCID: PMC3959687 DOI: 10.1161/jaha.113.000792] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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29
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Alvarez ML, Doné SC. SYBR® Green and TaqMan® quantitative PCR arrays: expression profile of genes relevant to a pathway or a disease state. Methods Mol Biol 2014; 1182:321-59. [PMID: 25055922 DOI: 10.1007/978-1-4939-1062-5_27] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Quantitative PCR arrays are the most reliable and accurate tool for analyzing the expression of a focused panel of genes relevant to a pathway or a disease state. PCR arrays allow gene expression analysis with the sensitivity, dynamic range, and specificity of a real-time PCR as well as the multi-gene profiling capability of a microarray. Differences among real-time PCR kits used in PCR arrays are largely restricted to the DNA polymerases and the detection methods used. In this chapter, we provide a step-by-step protocol for the two detection methods most commonly used in PCR arrays, known as SYBR(®) Green and TaqMan(®), which are based on two different approaches to detect PCR products. While SYBR(®) Green uses a binding dye that intercalates nonspecifically into double-stranded DNA, the TaqMan(®) approach relies on a fluorogenic oligonucleotide probe that binds only the DNA sequence between the two PCR primers. Therefore, only specific PCR product can generate a fluorescent signal in TaqMan(®) PCR. Here we also provide a comparison of the SYBR(®) Green and TaqMan(®) approaches and highlight their advantages and disadvantages to help the user to choose the best platform.
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Affiliation(s)
- M Lucrecia Alvarez
- Diabetes, Cardiovascular, and Metabolic Diseases, Translational Genomics Research Institute, 445 Fifth Street, Phoenix, AZ, 85004, USA,
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Cao H, Shockey JM, Klasson KT, Chapital DC, Mason CB, Scheffler BE. Developmental regulation of diacylglycerol acyltransferase family gene expression in tung tree tissues. PLoS One 2013; 8:e76946. [PMID: 24146944 PMCID: PMC3795650 DOI: 10.1371/journal.pone.0076946] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2013] [Accepted: 08/26/2013] [Indexed: 11/29/2022] Open
Abstract
Diacylglycerol acyltransferases (DGAT) catalyze the final and rate-limiting step of triacylglycerol (TAG) biosynthesis in eukaryotic organisms. DGAT genes have been identified in numerous organisms. Multiple isoforms of DGAT are present in eukaryotes. We previously cloned DGAT1 and DGAT2 genes of tung tree (Vernicia fordii), whose novel seed TAGs are useful in a wide range of industrial applications. The objective of this study was to understand the developmental regulation of DGAT family gene expression in tung tree. To this end, we first cloned a tung tree gene encoding DGAT3, a putatively soluble form of DGAT that possesses 11 completely conserved amino acid residues shared among 27 DGAT3s from 19 plant species. Unlike DGAT1 and DGAT2 subfamilies, DGAT3 is absent from animals. We then used TaqMan and SYBR Green quantitative real-time PCR, along with northern and western blotting, to study the expression patterns of the three DGAT genes in tung tree tissues. Expression results demonstrate that 1) all three isoforms of DGAT genes are expressed in developing seeds, leaves and flowers; 2) DGAT2 is the major DGAT mRNA in tung seeds, whose expression profile is well-coordinated with the oil profile in developing tung seeds; and 3) DGAT3 is the major form of DGAT mRNA in tung leaves, flowers and immature seeds prior to active tung oil biosynthesis. These results suggest that DGAT2 is probably the major TAG biosynthetic isoform in tung seeds and that DGAT3 gene likely plays a significant role in TAG metabolism in other tissues. Therefore, DGAT2 should be a primary target for tung oil engineering in transgenic organisms.
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Affiliation(s)
- Heping Cao
- U.S. Department of Agriculture, Agricultural Research Service, Southern Regional Research Center, Commodity Utilization Research Unit, New Orleans, Louisiana, United States of America
- * E-mail:
| | - Jay M. Shockey
- U.S. Department of Agriculture, Agricultural Research Service, Southern Regional Research Center, Commodity Utilization Research Unit, New Orleans, Louisiana, United States of America
| | - K. Thomas Klasson
- U.S. Department of Agriculture, Agricultural Research Service, Southern Regional Research Center, Commodity Utilization Research Unit, New Orleans, Louisiana, United States of America
| | - Dorselyn C. Chapital
- U.S. Department of Agriculture, Agricultural Research Service, Southern Regional Research Center, Commodity Utilization Research Unit, New Orleans, Louisiana, United States of America
| | - Catherine B. Mason
- U.S. Department of Agriculture, Agricultural Research Service, Southern Regional Research Center, Commodity Utilization Research Unit, New Orleans, Louisiana, United States of America
| | - Brian E. Scheffler
- U.S. Department of Agriculture, Agricultural Research Service, Genomics and Bioinformatics Research Unit, Stoneville, Mississippi, United States of America
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31
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Cao H, Cao F, Roussel AM, Anderson RA. Quantitative PCR for glucose transporter and tristetraprolin family gene expression in cultured mouse adipocytes and macrophages. In Vitro Cell Dev Biol Anim 2013; 49:759-70. [PMID: 23949780 DOI: 10.1007/s11626-013-9671-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2013] [Accepted: 07/17/2013] [Indexed: 01/24/2023]
Abstract
Quantitative real-time PCR (qPCR) such as TaqMan and SYBR Green qPCR are widely used for gene expression analysis. The drawbacks of SYBR Green assay are that the dye binds to any double-stranded DNA which can generate false-positive signals and that the length of the amplicon affects the intensity of the amplification. Previous results demonstrate that TaqMan assay is more sensitive but generates lower calculated expression levels than SYBR Green assay in quantifying seven mRNAs in tung tree tissues. The objective of this study is to expand the analysis using animal cells. We compared both qPCR assays for quantifying 24 mRNAs including those coding for glucose transporter (Glut) and mRNA-binding protein tristetraprolin (TTP) in mouse 3T3-L1 adipocytes and RAW264.7 macrophages. The results showed that SYBR Green and TaqMan qPCR were reliable for quantitative gene expression in animal cells. This result was supported by validation analysis of Glut and TTP family gene expression. However, SYBR Green qPCR overestimated the expression levels in most of the genes tested. Finally, both qPCR instruments (Bio-Rad's CFX96 real-time system and Applied Biosystems' Prism 7700 real-time PCR instrument) generated similar gene expression profiles in the mouse cells. These results support the conclusion that both qPCR assays (TaqMan and SYBR Green qPCR) and both qPCR instruments (Bio-Rad's CFX96 real-time system and Applied Biosystems' Prism 7700 real-time PCR instrument) are reliable for quantitative gene expression analyses in animal cells but SYBR Green qPCR generally overestimates gene expression levels than TaqMan qPCR.
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Affiliation(s)
- Heping Cao
- U.S. Department of Agriculture-Agricultural Research Service, Southern Regional Research Center, 1100 Robert E. Lee Blvd, New Orleans, LA, 70124, USA,
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A generalized mathematical model to estimate T- and B-cell receptor diversities using AmpliCot. Biophys J 2013; 103:999-1010. [PMID: 23009849 DOI: 10.1016/j.bpj.2012.07.017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2012] [Revised: 05/14/2012] [Accepted: 07/16/2012] [Indexed: 11/20/2022] Open
Abstract
The efficiency of the adaptive immune system is dependent on the diversity of T- and B-cell receptors, which is created by random rearrangement of receptor gene segments. AmpliCot is an experimental technique that allows the measurement of the diversity of the T- and B-cell repertoire. This procedure has the advantage over other cloning and sequencing techniques of being time- and expense-effective. In previous studies, receptor diversity, measured with AmpliCot, has been inferred assuming a second-order kinetics model. The latter implies that the relation between diversity and concentration × time (Cot) values is linear. We show that a more detailed model, involving heteroduplex and transient-duplex formation, leads to significantly better fits of experimental data and to nonlinear diversity-Cot relations. We propose an alternative fitting procedure, which is straightforward to apply and which gives an improved description of the relationship between Cot values and diversity.
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33
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Yi C, Hong Y. Estimating the copy number of transgenes in transformed cotton by real-time quantitative PCR. Methods Mol Biol 2013; 958:109-30. [PMID: 23143487 DOI: 10.1007/978-1-62703-212-4_9] [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: 05/11/2023]
Abstract
Transgenic cotton has widely been employed both in commercial cultivation and basic research. It is essential to determine which plants contain the transgene and in how many copies after transgenic cotton plants are generated. A TaqMan quantitative real-time polymerase chain reaction (Tq RT-PCR) method is described here to examine transgene copy number in transgenic cotton plants. The estimation of two transgene elements, the target gene of green fluorescence protein (GFP) and the selective gene of neomycin phosphotransferase II (NPTII), is used as an example to detail each step in Tq RT-PCR procedure, including endogenous reference gene selection, reference plasmid construction, primer-probe design, DNA extraction, real-time PCR, and data analysis. Comparing with traditional approach-Southern hybridization -analysis, this method can be used efficiently in screening large number of T0 transgenic cotton plants at early stage of transformation process as well as identifying transgene homozygotes in a segregation population.
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Affiliation(s)
- Chengxin Yi
- JOil (S) Pte Ltd, 1 Research Link, National University of Singapore, Singapore, Singapore
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34
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Cao H, Shockey JM. Comparison of TaqMan and SYBR Green qPCR methods for quantitative gene expression in tung tree tissues. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2012; 60:12296-303. [PMID: 23176309 DOI: 10.1021/jf304690e] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Quantitative real-time-PCR (qPCR) is widely used for gene expression analysis due to its large dynamic range, tremendous sensitivity, high sequence specificity, little to no postamplification processing, and sample throughput. TaqMan and SYBR Green qPCR are two frequently used methods. However, direct comparison of both methods using the same primers and biological samples is still limited. We compared both assays using seven RNAs from the seeds, leaves, and flowers of tung tree (Vernicia fordii), which produces high-value industrial oil. High-quality RNA were isolated from tung tissues, as indicated by a high rRNA ratio and RNA integrity number. qPCR primers and TaqMan probes were optimized. Under optimized conditions, both qPCR gave high correlation coefficiency and similar amplification efficiency, but TaqMan qPCR generated higher y-intercepts than SYBR Green qPCR, which overestimated the expression levels regardless of the genes and tissues tested. This is validated using well-known Dgat2 and Fadx gene expression in tung tissues. The results demonstrate that both assays are reliable for determining gene expression in tung tissues and that the TaqMan assay is more sensitive but generates lower calculated expression levels than the SYBR Green assay. This study suggests that any discussion of gene expression levels needs to be linked to which qPCR method is used in the analysis.
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Affiliation(s)
- Heping Cao
- U.S. Department of Agriculture, New Orleans, LA 70124, USA.
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35
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[Letter to the editor] Combined FAM-labeled TaqMan probe detection and SYBR green I melting curve analysis in multiprobe qPCR genotyping assays. Biotechniques 2012; 52:81-6. [PMID: 22313405 DOI: 10.2144/000113808] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2011] [Accepted: 12/19/2011] [Indexed: 11/23/2022] Open
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Thomsen N, Ali RG, Ahmed JN, Arkell RM. High resolution melt analysis (HRMA); a viable alternative to agarose gel electrophoresis for mouse genotyping. PLoS One 2012; 7:e45252. [PMID: 23028882 PMCID: PMC3446988 DOI: 10.1371/journal.pone.0045252] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2012] [Accepted: 08/14/2012] [Indexed: 11/24/2022] Open
Abstract
Most mouse genetics laboratories maintain mouse strains that require genotyping in order to identify the genetically modified animals. The plethora of mutagenesis strategies and publicly available mouse alleles means that any one laboratory may maintain alleles with random or targeted insertions of orthologous or unrelated sequences as well as random or targeted deletions and point mutants. Many experiments require that different strains be cross bred conferring the need to genotype progeny at more than one locus. In contrast to the range of new technologies for mouse mutagenesis, genotyping methods have remained relatively static with alleles typically discriminated by agarose gel electrophoresis of PCR products. This requires a large amount of researcher time. Additionally it is susceptible to contamination of future genotyping experiments because it requires that tubes containing PCR products be opened for analysis. Progress has been made with the genotyping of mouse point mutants because a range of new high-throughput techniques have been developed for the detection of Single Nucleotide Polymorphisms. Some of these techniques are suitable for genotyping point mutants but do not detect insertion or deletion alleles. Ideally, mouse genetics laboratories would use a single, high-throughput platform that enables closed-tube analysis to genotype the entire range of possible insertion and deletion alleles and point mutants. Here we show that High Resolution Melt Analysis meets these criteria, it is suitable for closed-tube genotyping of all allele types and current genotyping assays can be converted to this technology with little or no effort.
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Affiliation(s)
- Nicole Thomsen
- Early Mammalian Development Laboratory, Research School of Biology, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Radiya G. Ali
- Early Mammalian Development Laboratory, Research School of Biology, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Jehangir N. Ahmed
- Early Mammalian Development Laboratory, Research School of Biology, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Ruth M. Arkell
- Early Mammalian Development Laboratory, Research School of Biology, The Australian National University, Canberra, Australian Capital Territory, Australia
- * E-mail:
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37
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Lee MK, Kim HR. [Comparison between Real-Time PCR and Agarose Gel Electrophoresis for DNA Quantification.]. Korean J Lab Med 2012; 26:217-22. [PMID: 18156728 DOI: 10.3343/kjlm.2006.26.3.217] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Real-time polymerase chain reaction (PCR) is generally regarded as a very accurate and time-saving method, but it is expensive to run. We evaluated the reliability of an inexpensive and a researcher-friendly gel electrophoresis-based PCR method for the quantification of mRNA, and the results were compared with those obtained by real-time PCR. METHODS We compared the results of relative quantification for MMP-1 measured by real-time PCR and by ethidium bromide stained-agarose gel electrophoresis after end-point PCR. RESULTS There was significant but very weak correlation between real-time PCR and end-point PCR for relative quantification of MMP-1 (r=0.16, P<0.01). CONCLUSIONS Our results suggest that the use of the gel electrophoresis-based end-point PCR is inappropriate for quantifying mRNA. Therefore, in order to confirm the result of relative quantification by end-point PCR, the newly established real-time PCR method or northern hybridization should be applied.
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Affiliation(s)
- Mi Kyung Lee
- Department of Laboratory Medicine, College of Medicine, Chung-Ang University, Seoul, Korea.
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38
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SYBR Green I: fluorescence properties and interaction with DNA. J Fluoresc 2012; 22:1189-99. [PMID: 22534954 DOI: 10.1007/s10895-012-1059-8] [Citation(s) in RCA: 166] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2012] [Accepted: 04/09/2012] [Indexed: 10/28/2022]
Abstract
In this study, we have investigated the fluorescence properties of SYBR Green I (SG) dye and its interaction with double-stranded DNA (dsDNA). SG/dsDNA complexes were studied using various spectroscopic techniques, including fluorescence resonance energy transfer and time-resolved fluorescence techniques. It is shown that SG quenching in the free state has an intrinsic intramolecular origin; thus, the observed >1,000-fold SG fluorescence enhancement in complex with DNA can be explained by a dampening of its intra-molecular motions. Analysis of the obtained SG/DNA binding isotherms in solutions of different ionic strength and of SG/DNA association in the presence of a DNA minor groove binder, Hoechst 33258, revealed multiple modes of interaction of SG inner groups with DNA. In addition to interaction within the DNA minor groove, both intercalation between base pairs and stabilization of the electrostatic SG/DNA complex contributed to increased SG affinity to double-stranded DNA. We show that both fluorescence and the excited state lifetime of SG dramatically increase in viscous solvents, demonstrating an approximate 200-fold enhancement in 100 % glycerol, compared to water, which also makes SG a prospective fluorescent viscosity probe. A proposed structural model of the SG/DNA complex is compared and discussed with results recently reported for the closely related PicoGreen chromophore.
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Izumikawa M, Hayashi K, Polan MAA, Tang J, Saito T. Effects of amelogenin on proliferation, differentiation, and mineralization of rat bone marrow mesenchymal stem cells in vitro. ScientificWorldJournal 2012; 2012:879731. [PMID: 22547998 PMCID: PMC3322511 DOI: 10.1100/2012/879731] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2011] [Accepted: 10/20/2011] [Indexed: 11/17/2022] Open
Abstract
The aim of this study was to clarify the function of amelogenin, the major protein of enamel matrix derivative, on the proliferation, differentiation, and mineralization of cultured rat bone marrow stem cells (BMSCs), toward the establishment of future bone regenerative therapies. No differences in the morphology of BMSCs or in cell numbers were found between amelogenin addition and additive-free groups. The promotion of ALPase activity and the formation of mineralized nodules were detected at an early stage in amelogenin addition group. In quantitative real-time RT-PCR, mRNA expression of osteopontin, osteonectin, and type I collagen was promoted for 0.5 hours and 24 hours by addition of amelogenin. The mRNA expression of osteocalcin and DMP-1 was also stimulated for 24 hours and 0.5 hours, respectively, in amelogenin addition group. These findings clearly indicate that amelogenin promoted the differentiation and mineralization of rat BMSCs but did not affect cell proliferation or cell morphology.
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Affiliation(s)
- Masanobu Izumikawa
- Division of Clinical Cariology and Endodontology, Department of Oral Rehabilitation, School of Dentistry, Health Sciences University of Hokkaido, 1757 Tobetsu, Hokkaido 061-0293, Japan
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40
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Aldridge S, Hadfield J. Introduction to miRNA profiling technologies and cross-platform comparison. Methods Mol Biol 2012; 822:19-31. [PMID: 22144189 DOI: 10.1007/978-1-61779-427-8_2] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
MicroRNA analysis has been widely adopted for basic and applied science. The tools and technologies available for quantifying and analysing miRNAs are still maturing. Here, we give an introductory overview of the main tools and the challenges in their use. We also discuss the importance of basic experimental design, sample handling and analysis methods as the impact of these can be as profound as the choice of miRNA analysis platform. Whether the reader is interested in a gene-by-gene or genome-wide approach choosing the platform to use is not trivial. Careful thought given before starting an experiment will make the execution much easier.
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Thermodynamic and structural study of phenanthroline derivative ruthenium complex/DNA interactions: Probing partial intercalation and binding properties. J Inorg Biochem 2012; 106:1-9. [DOI: 10.1016/j.jinorgbio.2011.09.028] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2011] [Revised: 09/19/2011] [Accepted: 09/19/2011] [Indexed: 11/22/2022]
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Schallon A, Synatschke CV, Pergushov DV, Jérôme V, Müller AHE, Freitag R. DNA melting temperature assay for assessing the stability of DNA polyplexes intended for nonviral gene delivery. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2011; 27:12042-51. [PMID: 21770418 DOI: 10.1021/la201803c] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Many synthetic polycations have the ability to form complexes with the polyanion DNA, yet only a few, most notably poly(ethylene imine) (PEI), are efficient gene-delivery vehicles. Although a common explanation of this observation relies on the buffering capacity of the polycation, the intracellular stability of the complex may also play a role and should not be neglected. Assays typically used to follow complex formation, however, often do not provide the required information on stability. In this article, we propose the change in the DNA melting temperature observable after complex formation to be a significant indicator of complex stability. For a given DNA/polycation ratio, changes in the melting temperature are shown to depend on the polycation chemistry but not on the DNA topology or the polycation architecture. Effects of changes in the DNA/polycation ratio as well as the effect of polycation quaternization can be interpreted using the melting temperature assay. Finally, the assay was used to follow the displacement of DNA from the complexes by poly(methacrylic acid) or short single-stranded DNA sequences as competing polyanions.
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Affiliation(s)
- Anja Schallon
- Chair for Process Biotechnology, University of Bayreuth, Germany
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Schoen I, Ries J, Klotzsch E, Ewers H, Vogel V. Binding-activated localization microscopy of DNA structures. NANO LETTERS 2011; 11:4008-11. [PMID: 21838238 DOI: 10.1021/nl2025954] [Citation(s) in RCA: 115] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Many nucleic acid stains show a strong fluorescence enhancement upon binding to double-stranded DNA. Here we exploit this property to perform superresolution microscopy based on the localization of individual binding events. The dynamic labeling scheme and the optimization of fluorophore brightness yielded a resolution of ∼14 nm (fwhm) and a spatial sampling of 1/nm. We illustrate our approach with two different DNA-binding dyes and apply it to visualize the organization of the bacterial chromosome in fixed Escherichia coli cells. In general, the principle of binding-activated localization microscopy (BALM) can be extended to other dyes and targets such as protein structures.
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Affiliation(s)
- Ingmar Schoen
- Laboratory for Biologically Oriented Materials, ETH Zurich, Zurich, Switzerland.
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Koppelkamm A, Vennemann B, Lutz-Bonengel S, Fracasso T, Vennemann M. RNA integrity in post-mortem samples: influencing parameters and implications on RT-qPCR assays. Int J Legal Med 2011; 125:573-80. [PMID: 21584656 DOI: 10.1007/s00414-011-0578-1] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2010] [Accepted: 04/29/2011] [Indexed: 01/27/2023]
Abstract
Messenger RNA (mRNA) profiling in post-mortem human tissue might reveal information about gene expression at the time point of death or close to it. When working with post-mortem human tissue, one is confronted with a natural RNA degradation caused by several parameters which are not yet fully understood. The aims of the present study were to analyse the influence of impaired RNA integrity on the reliability of quantitative gene expression data and to identify ante- and post-mortem parameters that might lead to reduced RNA integrities in post-mortem human brain, cardiac muscle and skeletal muscle tissues. Furthermore, this study determined the impact of several parameters like type of tissue, age at death, gender and body mass index (BMI), as well as duration of agony, cause of death and post-mortem interval on the RNA integrity. The influence of RNA integrity on the reliability of quantitative gene expression data was analysed by generating degradation profiles for three gene transcripts. Based on the deduced cycle of quantification data, this study shows that reverse transcription quantitative polymerase chain reaction (RT-qPCR) performance is affected by impaired RNA integrity. Depending on the transcript and tissue type, a shift in cycle threshold values of up to two cycles was observed. Determining RNA integrity number of 136 post-mortem samples revealed significantly different RNA qualities among the three tissue types with brain revealing significantly lower integrities compared to skeletal and cardiac muscle. The body mass index was found to influence RNA integrity in skeletal muscle tissue (M. iliopsoas). Samples originating from deceased with a BMI > 25 were of significantly lower integrity compared to samples from normal weight donors. Correct data normalisation was found to partly diminish the effects caused by impaired RNA quality. Nevertheless, it can be concluded that in post-mortem tissue with low RNA integrity numbers, the detection of large differences in gene expression activities might still be possible, whereas small expression differences are prone to misinterpretation due to degradation. Thus, when working with post-mortem samples, we recommend generating degradation profiles for all transcripts of interest in order to reveal detection limits of RT-qPCR assays.
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Affiliation(s)
- Antje Koppelkamm
- Institute of Legal Medicine, Freiburg University Medical Center, Albertstrasse 9, 79104 Freiburg, Germany
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Affiliation(s)
- John J. Maurer
- Department of Population Health, The University of Georgia, Athens, Georgia 30602
- Center for Food Safety, The University of Georgia, Griffin, Georgia 30223;
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Dragan AI, Casas-Finet JR, Bishop ES, Strouse RJ, Schenerman MA, Geddes CD. Characterization of PicoGreen interaction with dsDNA and the origin of its fluorescence enhancement upon binding. Biophys J 2011; 99:3010-9. [PMID: 21044599 DOI: 10.1016/j.bpj.2010.09.012] [Citation(s) in RCA: 126] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2010] [Revised: 07/26/2010] [Accepted: 09/03/2010] [Indexed: 11/17/2022] Open
Abstract
PicoGreen is a fluorescent probe that binds dsDNA and forms a highly luminescent complex when compared to the free dye in solution. This unique probe is widely used in DNA quantitation assays but has limited application in biophysical analysis of DNA and DNA-protein systems due to limited knowledge pertaining to its physical properties and characteristics of DNA binding. Here we have investigated PicoGreen binding to DNA to reveal the origin and mode of PicoGreen/DNA interactions, in particular the role of electrostatic and nonelectrostatic interactions in formation of the complex, as well as demonstrating minor groove binding specificity. Analysis of the fluorescence properties of free PicoGreen, the diffusion properties of PG/DNA complexes, and the excited-state lifetime changes upon DNA binding and change in solvent polarity, as well as the viscosity, reveal that quenching of PicoGreen in the free state results from its intramolecular dynamic fluctuations. On binding to DNA, intercalation and electrostatic interactions immobilize the dye molecule, resulting in a >1000-fold enhancement in its fluorescence. Based on the results of this study, a model of PicoGreen/DNA complex formation is proposed.
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Affiliation(s)
- A I Dragan
- Institute of Fluorescence, University of Maryland, Baltimore County, Maryland, USA
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Matsumoto Y, Ishida T, Takeda T, Koga T, Fujii M, Ishii Y, Fujimura Y, Miura D, Wariishi H, Yamada H. Maternal exposure to dioxin reduces hypothalamic but not pituitary metabolome in fetal rats: a possible mechanism for a fetus-specific reduction in steroidogenesis. J Toxicol Sci 2010; 35:365-73. [PMID: 20519845 DOI: 10.2131/jts.35.365] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD) reduces the synthesis of pituitary gonadotropins in a fetal age-specific manner. The pituitary synthesis of gonadotropins is regulated by the hypothalamus and, thus, needs the differentiation and development of the hypothalamus requiring a number of factors including energy supply and neurotransmitters. To investigate the mechanism whereby TCDD reduces fetal gonadotropins, we carried out a comparative study on the metabolomes of the hypothalamus and pituitary using fetal and mature Wistar rats. Male fetuses at gestational day (GD)20 were removed from dams treated orally with TCDD (1 microg/kg) at GD15, and the metabolome profiles were analyzed by gas chromatography-mass spectrometry (GC-MS). The principal component analysis of GC-MS data revealed that TCDD caused a change in the profile of fetal metabolome more markedly in the hypothalamus than in the pituitary. In sharp contrast, TCDD did not cause any marked alteration in hypothalamic as well as pituitary metabolomes in male rats born of untreated dams and treated with TCDD at postnatal day 49. It was also demonstrated that a number of fetal hypothalamic components, including glutamine and gamma-aminobutyric acid, are reduced by TCDD. These results demonstrate a possibility that TCDD may reduce the metabolic activity of the hypothalamus in a fetus-specific fashion, resulting in the reduced synthesis of gonadotropins.
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Affiliation(s)
- Yuki Matsumoto
- Graduate School of Pharmaceutical Sciences, Kyushu University, Maidashi, Higashi-ku, Fukuoka, Japan.
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Grueso E, Prado-Gotor R. Thermodynamic and structural study of pyrene-1-carboxaldehyde/DNA interactions by molecular spectroscopy: Probing intercalation and binding properties. Chem Phys 2010. [DOI: 10.1016/j.chemphys.2010.05.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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49
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El-Shishtawy RM, Asiri AM, Basaif SA, Rashad Sobahi T. Synthesis of a new beta-naphthothiazole monomethine cyanine dye for the detection of DNA in aqueous solution. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2010; 75:1605-1609. [PMID: 20227908 DOI: 10.1016/j.saa.2010.02.026] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2009] [Revised: 01/22/2010] [Accepted: 02/11/2010] [Indexed: 05/28/2023]
Abstract
Novel monomethine cyanine dye (MC) derived from beta-naphthothiazole and benzothiazole has been prepared and characterized by (1)H and (13)C NMR, FTIR, ESIMS, elemental analyses, absorption and fluorescence spectroscopy. The dye was conveniently synthesized by the condensation of two sulfate heterocyclic quaternary salts. The interaction between calf thymus DNA (ct-DNA) in tris(hydroxymethyl)aminomethane-HCl (Tris-HCl) aqueous buffer solution and MC has been studied with spectral fluorescence method. The binding constant value has been determined by fluorescence titration of MC with ct-DNA concentrations. The result obtained is consistent with an intercalative binding interaction between MC and ct-DNA. Compared with ethidium bromide (EB), MC showed a huge fluorescence enhancement upon mixing with ct-DNA.
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Affiliation(s)
- Reda M El-Shishtawy
- Faculty of Science, Chemistry Department, King Abdul-Aziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia.
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Lezhava A, Ishidao T, Ishizu Y, Naito K, Hanami T, Katayama A, Kogo Y, Soma T, Ikeda S, Murakami K, Nogawa C, Itoh M, Mitani Y, Harbers M, Okamoto A, Hayashizaki Y. Exciton Primer-mediated SNP detection in SmartAmp2 reactions. Hum Mutat 2010; 31:208-17. [PMID: 20052755 DOI: 10.1002/humu.21177] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Most commonly used intercalating fluorescent dyes in DNA detection are lacking any sequence specificity, whereas so-called Exciton Primers can overcome this limitation by functioning as "sequence-specific dyes." After hybridization to complementary sequences, the fluorescence of Exciton Primers provides sequence-specific signals for real-time monitoring of amplification reactions. Applied to the SmartAmp2 mutation detection process, Exciton Primers show high signal strength with low background leading to a superior specificity and sensitivity compared to SYBR Green I. Signal strength can be further enhanced using multiple dyes within one Exciton Primer or use of multiple Exciton Primers in the same amplification reaction. Here we demonstrate the use of Exciton Primers for genotyping a single nucleotide polymorphism (SNP) in the VKORC1 locus (-1639G>A) relevant for Warfarin dosing as an example for Exciton Primers mediated genotyping by SmartAmp2. The genotyping assay can use only one labeled Exciton Primer for endpoint detection, or simultaneously by real-time monitoring detect wild-type and mutant alleles in a one-tube reaction using two Exciton Primers having different dyes. Working directly from blood samples, Exciton Primer mediated genotyping by SmartAmp2 offers superior solutions for rapid point-of-care testing.
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Affiliation(s)
- Alexander Lezhava
- Technology Development Unit, Omics Science Center (OSC), RIKEN Yokohama Institute, Kanagawa, Japan
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