1
|
Koo YK, Kwon SS, Suh EJ, Kim NH, Kim HK, Cho YK, Choi SJ, Kim S, Lee KA. Evaluating the TaqMan Jr a-Genotyping Method for Rapidly Predicting the Presence of Anti-Jr a Antibodies. Ann Lab Med 2024:alm.2023.0325. [PMID: 38373791 DOI: 10.3343/alm.2023.0325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 11/14/2023] [Accepted: 02/06/2024] [Indexed: 02/21/2024] Open
Abstract
Background The Jra antigen is a high-prevalence red blood cell (RBC) antigen. Reports on cases of fatal hemolytic disease of the fetus and newborn and acute hemolytic transfusion reactions suggest that antibodies against Jra (anti-Jra) have potential clinical significance. Identifying anti-Jra is challenging owing to a lack of commercially available antisera. We developed an alternative approach to rapidly predict the presence of anti-Jra using the TaqMan single-nucleotide polymorphism (SNP)-genotyping method. Methods Residual peripheral blood samples from 10 patients suspected of having the anti-Jra were collected. Two samples with confirmed Jr(a-) RBCs and anti-Jra were used to validate the TaqMan genotyping assay by comparing the genotyping results with direct sequencing. The accuracy of the assay in predicting the presence of anti-Jra was verified through crossmatching with in-house Jr(a-) O+ RBCs. Results The TaqMan-genotyping method was validated with two Jr(a-) RBC- and anti-Jra-confirmed samples that showed concordant Jra genotyping and direct sequencing results. Jra genotyping for the remaining samples and crossmatching the serum samples with in-house Jr(a-) O+ RBCs showed consistent results. Conclusions We validated a rapid, simple, accurate, and cost-effective method for predicting the presence of anti-Jra using a TaqMan-based SNP-genotyping assay. Implementing this method in routine practice in clinical laboratories will assist in solving difficult problems regarding alloantibodies to high-prevalence RBC antigens and ultimately aid in providing safe and timely transfusions and proper patient care.
Collapse
Affiliation(s)
- Yu-Kyung Koo
- Department of Laboratory Medicine, Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - Soon Sung Kwon
- Department of Laboratory Medicine, Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - Eun Jung Suh
- Department of Laboratory Medicine, Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - Na Hyeong Kim
- Department of Laboratory Medicine, Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - Hyun Kyung Kim
- Department of Laboratory Medicine, Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - Youn Keong Cho
- Department of Laboratory Medicine, Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - Seung Jun Choi
- Department of Laboratory Medicine, Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - Sinyoung Kim
- Department of Laboratory Medicine, Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - Kyung-A Lee
- Department of Laboratory Medicine, Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
| |
Collapse
|
2
|
Notsu K, El Daous H, Mitoma S, Norimine J, Sekiguchi S. A pooled testing system to rapidly identify cattle carrying the elite controller BoLA-DRB3*009:02 haplotype against bovine leukemia virus infection. HLA 2021; 99:12-24. [PMID: 34837483 PMCID: PMC9543338 DOI: 10.1111/tan.14502] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 11/16/2021] [Accepted: 11/24/2021] [Indexed: 11/30/2022]
Abstract
As genetically resistant individuals, the “elite controllers” (ECs) of human immunodeficiency virus infection have been focused on as the keys to developing further functional treatments in medicine. In the livestock production field, identifying the ECs of bovine leukemia virus (BLV) infection in cattle is desired to stop BLV transmission chains on farms. Cattle carrying the bovine leukocyte antigen (BoLA)‐DRB3*009:02 allele (DRB3*009:02) have a strong possibility of being BLV ECs. Most of cattle carrying this allele maintain undetectable BLV proviral loads and do not shed virus even when infected. BLV ECs can act as transmission barriers when placed between uninfected and infected cattle in a barn. To identify cattle carrying DRB3*009:02 in large populations more easily, we developed a pooled testing system. It employs a highly sensitive, specific real‐time PCR assay and TaqMan MGB probes (DRB3*009:02‐TaqMan assay). Using this system, we determined the percentage of DRB3*009:02‐carrying cattle on Kyushu Island, Japan. Our pooled testing system detected cattle carrying the DRB3*009:02 allele from a DNA pool containing one DRB3*009:02‐positive animal and 29 cattle with other alleles. Its capacity is sufficient for herd‐level screening for DRB3*009:02‐carrying cattle. The DRB3*009:02‐TaqMan assay showed high‐discriminative sensitivity and specificity toward DRB3*009:02, making it suitable for identifying DRB3*009:02‐carrying cattle in post‐screening tests on individuals. We determined that the percentage of DRB3*009:02‐carrying cattle in Kyushu Island was 10.56%. With its ease of use and reliable detection, this new method strengthens the laboratory typing for DRB3*009:02‐carrying cattle. Thus, our findings support the use of BLV ECs in the field.
Collapse
Affiliation(s)
- Kosuke Notsu
- Graduate School of Medicine and Veterinary Medicine, University of Miyazaki, Miyazaki, Japan
| | - Hala El Daous
- Graduate School of Medicine and Veterinary Medicine, University of Miyazaki, Miyazaki, Japan.,Faculty of Veterinary Medicine, Benha University, Toukh, Egypt
| | - Shuya Mitoma
- Graduate School of Medicine and Veterinary Medicine, University of Miyazaki, Miyazaki, Japan
| | - Junzo Norimine
- Department of Veterinary Science, Faculty of Agriculture, University of Miyazaki, Miyazaki, Japan.,Center for Animal Disease Control, University of Miyazaki, Miyazaki, Japan
| | - Satoshi Sekiguchi
- Department of Veterinary Science, Faculty of Agriculture, University of Miyazaki, Miyazaki, Japan.,Center for Animal Disease Control, University of Miyazaki, Miyazaki, Japan
| |
Collapse
|
3
|
Liu F, Cheng J, Liu X, Wang XQ. High-Throughput and Accurate Determination of Transgene Copy Number and Zygosity in Transgenic Maize: From DNA Extraction to Data Analysis. Int J Mol Sci 2021; 22:12487. [PMID: 34830369 DOI: 10.3390/ijms222212487] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Revised: 11/10/2021] [Accepted: 11/10/2021] [Indexed: 11/16/2022] Open
Abstract
It is vital to develop high-throughput methods to determine transgene copy numbers initially and zygosity during subsequent breeding. In this study, the target sequence of the previously reported endogenous reference gene hmg was analyzed using 633 maize inbred lines, and two SNPs were observed. These SNPs significantly increased the PCR efficiency, while the newly developed hmg gene assay (hmg-taq-F2/R2) excluding these SNPs reduced the efficiency into normal ranges. The TaqMan amplification efficiency of bar and hmg with newly developed primers was calculated as 0.993 and 1.000, respectively. The inter-assay coefficient of variation (CV) values for the bar and hmg genes varied from 1.18 to 2.94%. The copy numbers of the transgene bar using new TaqMan assays were identical to those using dPCR. Significantly, the precision of one repetition reached 96.7% of that of three repetitions of single-copy plants analyzed by simple random sampling, and the actual accuracy reached 95.8%, confirmed by T1 and T2 progeny. With the high-throughput DNA extraction and automated data analysis procedures developed in this study, nearly 2700 samples could be analyzed within eight hours by two persons. The combined results suggested that the new hmg gene assay developed here could be a universal maize reference gene system, and the new assay has high throughput and high accuracy for large-scale screening of maize varieties around the world.
Collapse
|
4
|
Mahajan S, Sharma GK, Subramaniam S, Biswal JK, Pattnaik B. Selective isolation of foot-and-mouth disease virus from coinfected samples containing more than one serotype. Braz J Microbiol 2021; 52:2447-54. [PMID: 34478107 DOI: 10.1007/s42770-021-00604-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 08/27/2021] [Indexed: 10/20/2022] Open
Abstract
The foot-and-mouth disease virus (FMDV) causes a highly infectious disease of all cloven-footed animals. The RNA genome of the virus continuously evolves, leading to the generation of new strains; this necessitates the selection of new vaccine strains to ensure complete protection. Infection with one FMDV serotype does not provide cross-protection against the other FMDV serotypes. Many of the recovered animals may become carriers of the FMDV, but they still remain susceptible to the other serotypes. Coinfection with multiple FMDV serotypes has been reported and studied to understand the virus evolution. Isolation and characterization of all the involved serotypes in the mixed infection case is essential to understand the molecular evolution of the virus. In this study, two cases of coinfection were studied by selective isolation of each of the FMDV serotypes under the cross-serotype-specific immune pressure. It was estimated that the virus present in a minimum of 10-0.92 TCID50 could be isolated from the mixed population containing other serotypes in infective doses of 100.25 TCID50 or less. All involved serotypes present in the mixed infection cases were isolated, without any cross-contamination. Virus characterization revealed that genotype 2 was of serotype A virus from a sample collected in 1995, which was last reported in 1986, indicating a possible subdued prevalence of the genetic group even after vanishing from the field.
Collapse
|
5
|
Isayama K, Watanabe K, Okamoto M, Murata T, Mizukami Y. Standardization of an LNA-based TaqMan assay qPCR analysis for Aspiculuris tetraptera DNA in mouse faeces. BMC Microbiol 2020; 20:371. [PMID: 33287731 PMCID: PMC7720592 DOI: 10.1186/s12866-020-02053-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 11/26/2020] [Indexed: 11/24/2022] Open
Abstract
Background Aspiculuris tetraptera, as a parasitic pinworm, is most frequently detected in laboratory mice, and transmission is mediated by the eggs contained in the faeces of infected mice. A highly sensitive and quantitative faeces-based diagnostic tool would be useful for the early detection of A. tetraptera to inhibit the expansion of infection. In this study, we developed a quantitative assay that exhibits high sensitivity in detecting A. tetraptera in faeces using PCR techniques. Results Endpoint PCR demonstrated the detection of A. tetraptera DNA in 0.5 ng genomic DNA extracted from the faeces of infected mice. To quantitatively detect the small amount of A. tetraptera DNA, locked nucleic acid (LNA)-based primers and LNA-based TaqMan probes were used for the quantitative PCR assay (qPCR). The combination of LNA-based DNA increased detection sensitivity by more than 100-fold compared to using normal oligo DNAs. The copy number of the A. tetraptera DNA detected was positively related to the infected faeces-derived genomic DNA with a simple linearity regression in the range of 20 pg to 15 ng of the genomic DNA. To more conveniently detect infection using faeces, the LNA-based TaqMan assay was applied to the crude fraction of the faeces without DNA purification. An assay using ethanol precipitation of the faeces yielded results consistent with those of direct microscopic observation. Conclusion The LNA-TaqMan assay developed in this study quantitatively detects A. tetraptera infection in mouse faeces. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-020-02053-6.
Collapse
Affiliation(s)
- Keishiro Isayama
- Institute of Laboratory Animals, Yamaguchi University Science Research Center, Yamaguchi, 755-8505, Japan
| | - Kenji Watanabe
- Institute of Gene Research, Yamaguchi University Science Research Center, Yamaguchi, 755-8505, Japan
| | - Mariko Okamoto
- Laboratory of Veterinary Immunology, School of Veterinary Medicine, Azabu University, Sagamihara, 252-5201, Japan
| | - Tomoaki Murata
- Institute of Laboratory Animals, Yamaguchi University Science Research Center, Yamaguchi, 755-8505, Japan
| | - Yoichi Mizukami
- Institute of Gene Research, Yamaguchi University Science Research Center, Yamaguchi, 755-8505, Japan.
| |
Collapse
|
6
|
Schneider B, Kätzel R, Kube M. Widespread occurrence of 'Candidatus Phytoplasma ulmi' in elm species in Germany. BMC Microbiol 2020; 20:74. [PMID: 32234008 PMCID: PMC7110721 DOI: 10.1186/s12866-020-01749-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 03/10/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND 'Candidatus Phytoplasma ulmi' is the agent associated with elm yellows and has been categorised in the European Union as a quarantine pathogen. For central and northern European countries, information on the occurrence and distribution of the pathogen and its impact on elms is scarce, so a survey of native elm trees has been conducted in Germany. RESULTS About 6500 samples from Ulmus minor, Ulmus laevis and Ulmus glabra, were collected nationwide. Phytoplasma detection was performed by applying a universal 16Sr DNA-based quantitative PCR (qPCR) assay and a novel 'Ca. P. ulmi' specific qPCR assay targeting the 16S-23S spacer region. Both assays revealed that 28% of the samples were infected by 'Ca. P. ulmi', but infection rates of the elm species and regional incidences differed. The phytoplasma presence in the trees was not correlated to disease-specific symptoms. The survey identified a regional disparity of infection which was high in east, south and central Germany, whereas only a few infected sites were found in the western and northern parts of the country. Monitoring the seasonal titre of 'Ca. P. ulmi' in an infected tree by qPCR revealed a high colonisation in all parts of the tree throughout the year. CONCLUSIONS 'Ca. P. ulmi' is widely present in elms in Germany. The rare occurrence of symptoms indicates either a high degree of tolerance in elm populations or a low virulence of pathogen strains enabling high infection rates in a long-living host.
Collapse
Affiliation(s)
- Bernd Schneider
- Thuenen-Institute of Forest Genetics, Eberswalder Chaussee 3A, 15377 Waldsieversdorf, Germany.
| | - Ralf Kätzel
- Landeskompetenzzentrum Forst Eberswalde, Alfred-Möller-Straße 1, 16225, Eberswalde, Germany
| | - Michael Kube
- Department of Integrative Infection Biology Crops-Livestock, University of Hohenheim, Garbenstr. 30, 70599, Stuttgart, Germany
| |
Collapse
|
7
|
Alshanbari F, Castaneda C, Juras R, Hillhouse A, Mendoza MN, Gutiérrez GA, Ponce de León FA, Raudsepp T. Comparative FISH-Mapping of MC1R, ASIP, and TYRP1 in New and Old World Camelids and Association Analysis With Coat Color Phenotypes in the Dromedary ( Camelus dromedarius). Front Genet 2019; 10:340. [PMID: 31040864 PMCID: PMC6477024 DOI: 10.3389/fgene.2019.00340] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 03/29/2019] [Indexed: 12/15/2022] Open
Abstract
Melanocortin 1 receptor (MC1R), the agouti signaling protein (ASIP), and tyrosinase related protein 1 (TYRP1) are among the major regulators of pigmentation in mammals. Recently, MC1R and ASIP sequence variants were associated with white and black/dark brown coat colors, respectively, in the dromedary. Here we confirmed this association by independent sequencing and mutation discovery of MC1R and ASIP coding regions and by TaqMan genotyping in 188 dromedaries from Saudi Arabia and United States, including 38 black, 53 white, and 97 beige/brown/red animals. We showed that heterozygosity for a missense mutation c.901C > T in MC1R is sufficient for the white coat color suggesting a possible dominant negative effect. Likewise, we confirmed that the majority of black dromedaries were homozygous for a frameshift mutation in ASIP exon 2, except for 4 animals, which were heterozygous. In search for additional mutations underlying the black color, we identified another frameshift mutation in ASIP exon 4 and 6 new variants in MC1R including a significantly associated SNP in 3'UTR. In pursuit of sequence variants that may modify dromedary wild-type color from dark-reddish brown to light beige, we identified 4 SNPs and one insertion in TYRP1 non-coding regions. However, none of these were associated with variations in wild-type colors. Finally, the three genes were cytogenetically mapped in New World (alpaca) and Old World (dromedary and Bactrian camel) camelids. The MC1R was assigned to chr21, ASIP to chr19 and TYRP1 to chr4 in all 3 species confirming extensive conservation of camelid karyotypes. Notably, while the locations of ASIP and TYRP1 were in agreement with human-camelid comparative map, mapping MC1R identified a new evolutionary conserved synteny segment between camelid chromosome 21 and HSA16. The findings contribute to coat color genomics and the development of molecular tests in camelids and toward the chromosome level reference assemblies of camelid genomes.
Collapse
Affiliation(s)
- Fahad Alshanbari
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, United States
| | - Caitlin Castaneda
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, United States
| | - Rytis Juras
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, United States
| | - Andrew Hillhouse
- Institute for Genome Sciences and Society, Texas A&M University, College Station, TX, United States
| | - Mayra N. Mendoza
- Animal Breeding Program, National Agrarian University La Molina, Lima, Peru
| | | | | | - Terje Raudsepp
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, United States
| |
Collapse
|
8
|
Almigbal TH, Batais MA, Hasanato RM, Alharbi FK, Khan IA, Alharbi KK. Role of Apolipoprotein E gene polymorphism in the risk of familial hypercholesterolemia: a case-control study. Acta Biochim Pol 2018; 65:415-420. [PMID: 30235358 DOI: 10.18388/abp.2017_2344] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Revised: 06/28/2018] [Accepted: 07/02/2018] [Indexed: 11/10/2022]
Abstract
Familial Hypercholesterolemia (FH) is characterized by elevated cholesterol and based on biochemical, clinical, and genetic studies and FH disease, which was documented even with limited mutations. Earlier studies focused on Apolipoprotein E (ApoE) in variable diseases. The current study aimed to investigate the genetic association between FH disease and ApoE gene polymorphisms (rs429358 and rs7412) in the Saudi population. This case-control study was a hospital-based study performed in Saudi Arabia. Two hundred and four subjects in total were recruited and consisted of FH participants (n=104) and the controls (n=100). Common polymorphisms of ApoE gene (rs429358 and rs7412) were chosen and subjected to the genotyping using the TaqMan assay. Moreover, the ApoE risk allele E4 was proved significantly associated with FH cases when compared with controls (OR-2.24 (95%CI: 1.06-4.70); p=0.02). Lipid profile parameters were significantly associated (p<0.05); however, the ApoE alleles and lipid profiles were not correlated (p>0.05). In conclusion, the FH case-control study was associated with the E4 allele in the Saudi population. However, E4 allele was appeared as a reliable risk marker for lipid profiles, but not for ApoE alleles.
Collapse
Affiliation(s)
- Turky H Almigbal
- Department of Family and Community Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Mohammed Ali Batais
- Department of Family and Community Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Rana M Hasanato
- Department of Pathology College of Medicine and University Hospitals, King Saud University, Riyadh, Kingdom of Saudi Arabia
| | - Fawaziah Khalaf Alharbi
- Department of Biology Science, College of Science and Arts, Al-Qassim University, Al-Qassim, Saudi Arabia
| | - Imran Ali Khan
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Saud University, PO Box-10219, Riyadh-11433, Kingdom of Saudi Arabia
| | - Khalid Khalaf Alharbi
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Saud University, PO Box-10219, Riyadh-11433, Kingdom of Saudi Arabia
| |
Collapse
|
9
|
van der Wolf JM, Evenhuis A, Kastelein P, Krijger MC, Funke VZ, van den Berg W, Moene AF. Risks for infection of strawberry plants with an aerosolized inoculum of Xanthomonas fragariae. Eur J Plant Pathol 2018; 152:711-722. [PMID: 30930545 PMCID: PMC6404663 DOI: 10.1007/s10658-018-1513-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Accepted: 05/23/2018] [Indexed: 06/09/2023]
Abstract
Xanthomonas fragariae is the causative agent of angular leaf spot of strawberry, a quarantine organism in plant propagation material in the European Union. Field experiments were conducted to assess the risks for infection of strawberry plants through dispersal of an aerosolized inoculum. In practice, pathogen aerosols can be formed during mowing of an infected crop or by water splashing on symptomatic plants during overhead irrigation or rain. In our experiments, aerosols were generated by spraying suspensions of X. fragariae with a density of 108 cfu ml-1 or water under pressure vertically up into the air. In strawberry plants (cv Elsanta) placed at 1.3, 5 and 10 m distance downwind from the spray boom, infections were found, as evidenced with a combination of dilution-plating and molecular techniques, but more frequently in plants wetted prior to inoculation than in plants kept dry. A logarithmic decrease in infection incidence was found with the distance to the inoculum source. Symptomatic plants were found up to 5 m distance from the inoculum source. No infected plants were found in plants placed 4 m upwind or treated with water. In glasshouse studies, it was shown that under conditions favorable for disease development, spray-inoculation of strawberry plants with estimated densities of X. fragariae as low as 2000 cfu per plant were able to cause symptoms both in cv Elsanta and cv Sonata. Results indicate that there is a considerable risk on infections of strawberry plants exposed to aerosolized inoculum.
Collapse
Affiliation(s)
- J. M. van der Wolf
- Wageningen University and Research, PO Box 16, 6700 Wageningen, AA Netherlands
| | - A. Evenhuis
- Wageningen University and Research, PO Box 16, 6700 Wageningen, AA Netherlands
| | - P. Kastelein
- Wageningen University and Research, PO Box 16, 6700 Wageningen, AA Netherlands
| | - M. C. Krijger
- Wageningen University and Research, PO Box 16, 6700 Wageningen, AA Netherlands
| | - V. Z. Funke
- Wageningen University and Research, PO Box 16, 6700 Wageningen, AA Netherlands
| | - W. van den Berg
- Wageningen University and Research, PO Box 16, 6700 Wageningen, AA Netherlands
| | - A. F. Moene
- Wageningen University and Research, PO Box 16, 6700 Wageningen, AA Netherlands
| |
Collapse
|
10
|
Fouad R, Zachariah K, Khairy M, Khorshied M, Ezzat W, Sheta MM, Heiba A. Single Nucleotide rs760370 Polymorphism at the Main Ribavirin Transporter Gene Detection by PCR-RFLP Assay Compared with the TaqMan Assay and Its Relation to Sustained Virological Response in Chronic HCV Patients Treated with Pegylated Interferon-Ribavirin Therapy. J Interferon Cytokine Res 2018; 37:90-96. [PMID: 28207300 DOI: 10.1089/jir.2016.0099] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Ribavirin clearly plays a role in chronic hepatitis C treatment response. The equilibrative nucleoside transporter-1 codified by SLC29A1 gene has been associated with ribavirin uptake into hepatocytes and erythrocytes. rs760370A>G single nucleotide polymorphism (SNP) at the SLC29A1 gene may have a role in ribavirin-based regimen treatment response. Accuracy of the polymerase-chain reaction-restriction fragment length polymorphism (PCR-RFLP) assay compared with the TaqMan assay for the detection of the SNP rs760370 at the main ribavirin transporter gene and its relation to sustained virological response in chronic hepatitis C virus (HCV) patients treated with pegylated interferon-ribavirin therapy. The study included 100 chronic HCV patients who were treated with pegylated interferon-ribavirin therapy. The patients were categorized according to the treatment response into responders (50 patients) and null responders (50 patients). rs760370 SNP was measured using TaqMan 5-nuclease assay and by the newly developed PCR-based RFLP assay. The overall accuracy of the newly developed PCR-RFLP assay compared with the TaqMan assay for rs760370 polymorphism detection was 100%. Allelic frequencies at rs760370 were as follows: A/A genotype (28%), A/G genotype (58%), and G/G genotype (14%). Treatment response was not significantly related with rs760370 polymorphism (P = 0.5). Ribavirin-induced anemia was good predictor of sustained virological response (P = 0.001), but was not related to rs760370 polymorphism (P = 0.92). PCR-RFLP assay is an accurate, cost-effective method in the detection of rs760370 compared with TaqMan assay. rs760370 SNP cannot serve as predictor of response in chronic HCV patients treated with interferon ribavirin therapy.
Collapse
Affiliation(s)
- Rabab Fouad
- 1 Endemic Medicine Department and Hepatology Unit, Faculty of Medicine, Cairo University , Cairo, Egypt
| | - Khaled Zachariah
- 1 Endemic Medicine Department and Hepatology Unit, Faculty of Medicine, Cairo University , Cairo, Egypt
| | - Marwa Khairy
- 1 Endemic Medicine Department and Hepatology Unit, Faculty of Medicine, Cairo University , Cairo, Egypt
| | - Mervat Khorshied
- 2 Clinical and Chemical Pathology Department, Faculty of Medicine, Cairo University , Cairo, Egypt
| | - Wafaa Ezzat
- 3 Topical Medicine Department, National Research Center, Cairo, Egypt
| | - Marwa M Sheta
- 2 Clinical and Chemical Pathology Department, Faculty of Medicine, Cairo University , Cairo, Egypt
| | - Ahmed Heiba
- 3 Topical Medicine Department, National Research Center, Cairo, Egypt
| |
Collapse
|
11
|
Afroj S, Aldahami K, Reddy G, Guard J, Adesiyun A, Samuel T, Abdela W. Simultaneous Detection of Multiple Salmonella Serovars from Milk and Chicken Meat by Real-Time PCR Using Unique Genomic Target Regions. J Food Prot 2017; 80:1944-1957. [PMID: 29058479 DOI: 10.4315/0362-028x.jfp-17-133] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 07/19/2017] [Indexed: 12/29/2022]
Abstract
A novel genomic and plasmid target-based PCR platform was developed for the detection of Salmonella serovars Heidelberg, Dublin, Hadar, Kentucky, and Enteritidis. Unique genome loci were obtained through extensive genome mining of protein databases and comparative genomic analysis of these serovars. Assays targeting Salmonella serovars Hadar, Heidelberg, Kentucky, and Dublin had 100% specificity and sensitivity, whereas those for Salmonella Enteritidis had 97% specificity and 88% sensitivity. The limits of detection for Salmonella serovars Heidelberg, Kentucky, Hadar, Enteritidis, and Dublin were 12, 9, 40, 13, and 5,280 CFU, respectively. A sensitivity assay was also performed by using milk artificially inoculated with pooled Salmonella serovars, yielding a detection limit of 1 to10 CFU/25 mL of milk samples after enrichment. The minimum DNA detected using the multiplexed TaqMan assay was 75.8 fg (1.53 × 101 genomic equivalents [GE]) for Salmonella Heidelberg, 140.8 fg (2.8 × 101 GE) for Salmonella Enteritidis, and 3.48 pg (6.96 × 102 GE) for Salmonella Dublin. PCR efficiencies were 89.8% for Salmonella Heidelberg, 94.5% for Salmonella Enteritidis, and 75.5% for Salmonella Dublin. Four types of 30 pasteurized milk samples were tested negative by culture techniques and with a genus-specific Salmonella invA gene PCR assay. Among 30 chicken samples similarly tested, 12 (40%) were positive by both culture and the invA PCR. Testing of these 12 samples with the serovar-specific PCR assay detected single and mixed contamination with Salmonella Kentucky, Salmonella Enteritidis, and Salmonella Heidelberg. Five unique primers were designed and tested by multiplex conventional PCR in conjunction with the use of the multiplex TaqMan assay with three of the primers. The diagnostic assays developed in this study could be used as tools for routine detection of these five Salmonella serovars and for epidemiological investigations of foodborne disease outbreaks.
Collapse
Affiliation(s)
- Sayma Afroj
- Department of Biology and.,Department of Pathobiology, College of Veterinary Medicine, Tuskegee University, Tuskegee, Alabama 36088, USA (ORCID: http://orcid.org/0000-0002-9262-5117 [W.A.]).,Cellular and Molecular Biosciences Program, Auburn University, Auburn, Alabama 36849, USA
| | - Khaled Aldahami
- Department of Pathobiology, College of Veterinary Medicine, Tuskegee University, Tuskegee, Alabama 36088, USA (ORCID: http://orcid.org/0000-0002-9262-5117 [W.A.])
| | - Gopal Reddy
- Department of Pathobiology, College of Veterinary Medicine, Tuskegee University, Tuskegee, Alabama 36088, USA (ORCID: http://orcid.org/0000-0002-9262-5117 [W.A.])
| | - Jean Guard
- U.S. Department of Agriculture, Agricultural Research Service, Athens, Georgia 30602, USA
| | - Abiodun Adesiyun
- School of Veterinary Medicine, Faculty of Medical Sciences, University of the West Indies, St. Augustine, Trinidad and Tobago
| | - Temesgen Samuel
- Department of Pathobiology, College of Veterinary Medicine, Tuskegee University, Tuskegee, Alabama 36088, USA (ORCID: http://orcid.org/0000-0002-9262-5117 [W.A.])
| | - Woubit Abdela
- Department of Pathobiology, College of Veterinary Medicine, Tuskegee University, Tuskegee, Alabama 36088, USA (ORCID: http://orcid.org/0000-0002-9262-5117 [W.A.])
| |
Collapse
|
12
|
Paik SH, Choi MR, Kwak SM, Bang SH, Chun JW, Kim JY, Choi J, Cho H, Jeong JE, Kim DJ. An association study of Taq1A ANKK1 and C957T and - 141C DRD2 polymorphisms in adults with internet gaming disorder: a pilot study. Ann Gen Psychiatry 2017; 16:45. [PMID: 29234453 PMCID: PMC5721653 DOI: 10.1186/s12991-017-0168-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 11/28/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Though Internet gaming disorder (IGD) is considered to share similar genetic vulnerability with substance addictions, little has been explored about the role of the genetic variants on IGD. This pilot study was designed to investigate the association of the Taq1A polymorphism of the ankyrin repeat and kinase domain containing 1 (ANKK1) gene and C957T and - 141C of the dopamine D2 receptor (DRD2) with IGD and their role on the personality and temperament traits in IGD among adult population. METHODS Sixty-three subjects with IGD and 87 control subjects who regularly played Internet games were recruited. Self-administered questionnaires on self-control, dysfunctional impulsivity, and temperament and character domains were done. The Taq1A ANKK1 and the C957T and - 141C ins/del from the DRD2 genes were genotyped using the specific TaqMan PCR assay. RESULTS The distributions of allele and genotype frequencies were not significantly different between the IGD and control groups in both genders. In male, excessive gaming and use of gaming to escape from a negative feeling were associated with the del- genotype of the - 141C. Among IGD, the del+ genotype was associated with higher novelty seeking. Logistic regression showed no predictive value of these polymorphisms for IGD when using age and gender as covariates. CONCLUSIONS Though no direct association of the Taq1A ANKK1 and C957T DRD2 variants with IGD were observed, the - 141C polymorphism may play a role in IGD via mediating symptoms or temperament traits.
Collapse
Affiliation(s)
- Soo-Hyun Paik
- Department of Psychiatry, Seoul St. Mary's Hospital, The Catholic University of Korea College of Medicine, Seoul, 222, Banpo-daero, Seocho-gu, Seoul, 06591 South Korea
| | - Mi Ran Choi
- Department of Psychiatry, Seoul St. Mary's Hospital, The Catholic University of Korea College of Medicine, Seoul, 222, Banpo-daero, Seocho-gu, Seoul, 06591 South Korea
| | - Su Min Kwak
- Department of Psychiatry, Seoul St. Mary's Hospital, The Catholic University of Korea College of Medicine, Seoul, 222, Banpo-daero, Seocho-gu, Seoul, 06591 South Korea
| | - Sol Hee Bang
- Department of Psychiatry, Seoul St. Mary's Hospital, The Catholic University of Korea College of Medicine, Seoul, 222, Banpo-daero, Seocho-gu, Seoul, 06591 South Korea
| | - Ji-Won Chun
- Department of Psychiatry, Seoul St. Mary's Hospital, The Catholic University of Korea College of Medicine, Seoul, 222, Banpo-daero, Seocho-gu, Seoul, 06591 South Korea
| | - Jin-Young Kim
- Department of Psychiatry, Seoul St. Mary's Hospital, The Catholic University of Korea College of Medicine, Seoul, 222, Banpo-daero, Seocho-gu, Seoul, 06591 South Korea
| | - Jihye Choi
- Department of Psychiatry, Seoul St. Mary's Hospital, The Catholic University of Korea College of Medicine, Seoul, 222, Banpo-daero, Seocho-gu, Seoul, 06591 South Korea
| | - Hyun Cho
- Department of Psychiatry, Seoul St. Mary's Hospital, The Catholic University of Korea College of Medicine, Seoul, 222, Banpo-daero, Seocho-gu, Seoul, 06591 South Korea
| | - Jo-Eun Jeong
- Department of Psychiatry, Seoul St. Mary's Hospital, The Catholic University of Korea College of Medicine, Seoul, 222, Banpo-daero, Seocho-gu, Seoul, 06591 South Korea
| | - Dai-Jin Kim
- Department of Psychiatry, Seoul St. Mary's Hospital, The Catholic University of Korea College of Medicine, Seoul, 222, Banpo-daero, Seocho-gu, Seoul, 06591 South Korea
| |
Collapse
|
13
|
Abstract
Real-time PCR-based genotyping methods, such as TaqMan allelic discrimination assays and allele-specific genotyping, are particularly useful when screening a handful of single nucleotide polymorphisms in hundreds of samples; either derived from different individuals, tissues, or pre-amplified DNA. Although real-time PCR-based methods such as TaqMan are well-established, alternative methods, like allele-specific genotyping, are powerful alternatives, especially for genotyping short tandem repeat (STR) length polymorphisms. Here, we describe all relevant aspects when developing an assay for a new SNP or STR using either TaqMan or allele-specific genotyping, respectively, such as primer and probe design, optimization of reaction conditions, the experimental procedure for typing hundreds of samples, and finally the data evaluation. Our goal is to provide a guideline for developing genotyping assays using these two approaches that render reliable and reproducible genotype calls involving minimal optimization.
Collapse
Affiliation(s)
- Angelika Heissl
- Institute of Biophysics, Johannes Kepler University, Gruberstraße 40, 4020, Linz, Austria
| | - Barbara Arbeithuber
- Institute of Biophysics, Johannes Kepler University, Gruberstraße 40, 4020, Linz, Austria
| | - Irene Tiemann-Boege
- Institute of Biophysics, Johannes Kepler University, Gruberstraße 40, 4020, Linz, Austria.
| |
Collapse
|
14
|
Shirafuji H, Yazaki R, Shuto Y, Yanase T, Kato T, Ishikura Y, Sakaguchi Z, Suzuki M, Yamakawa M. Broad-range detection of arboviruses belonging to Simbu serogroup lineage 1 and specific detection of Akabane, Aino and Peaton viruses by newly developed multiple TaqMan assays. J Virol Methods 2015; 225:9-15. [PMID: 26341063 DOI: 10.1016/j.jviromet.2015.08.021] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Revised: 08/30/2015] [Accepted: 08/30/2015] [Indexed: 12/22/2022]
Abstract
TaqMan assays were developed for the broad-range detection of arboviruses belonging to Simbu serogroup lineage 1 in the genus Orthobunyavirus and also for the specific detection of three viruses in the lineage, Akabane, Aino and Peaton viruses (AKAV, AINOV and PEAV, respectively). A primer and probe set was designed for the broad-range detection of Simbu serogroup lineage 1 (Pan-Simbu1 set) mainly targeting AKAV, AINOV, PEAV, Sathuperi and Shamonda viruses (SATV and SHAV), and the forward and reverse primers of the Pan-Simbu1 set were also used for the specific detection of AKAV with another probe (AKAV-specific set). In addition, two more primer and probe sets were designed for AINOV- and PEAV-specific detection, respectively (AINOV- and PEAV-specific sets). All of the four primer and probe sets successfully detected targeted viruses, and thus broad-range and specific detection of all the targeted viruses can be achieved by using two multiplex assays and a single assay in a dual (two-color) assay format when another primer and probe set for a bovine β-actin control is also used. The assays had an analytical sensitivity of 10 copies/tube for AKAV, at least 100 copies/tube for AINOV, 100 copies/tube for PEAV, one copy/tube for SATV and at least 10 copies/tube for SHAV, respectively. Diagnostic sensitivity of the assays was tested with field-collected bovine samples, and the results suggested that the sensitivity was higher than that of a conventional RT-PCR. These data indicate that the newly developed TaqMan assays will be useful tools for the diagnosis and screening of field-collected samples for infections of AKAV and several other arboviruses belonging to the Simbu serogroup lineage 1.
Collapse
Affiliation(s)
- Hiroaki Shirafuji
- Kyushu Research Station, National Institute of Animal Health (NIAH), National Agriculture and Food Research Organization (NARO), Japan.
| | - Ryu Yazaki
- Kusu Livestock Hygiene Service Center, Oita Prefectural Government, Japan
| | - Yozo Shuto
- Oita Livestock Hygiene Service Center, Oita Prefectural Government, Japan
| | - Tohru Yanase
- Kyushu Research Station, National Institute of Animal Health (NIAH), National Agriculture and Food Research Organization (NARO), Japan
| | - Tomoko Kato
- Kyushu Research Station, National Institute of Animal Health (NIAH), National Agriculture and Food Research Organization (NARO), Japan
| | - Youji Ishikura
- Domestic Livestock Disease Identification Office, Food Safety Promotion Division, Shimane Prefectural Government, Japan
| | - Zenjiro Sakaguchi
- Kagoshima Central Livestock Hygiene Service Center, Kagoshima Prefectural Government, Japan
| | - Moemi Suzuki
- Okinawa Prefectural Institute of Animal Health, Okinawa Prefectural Government, Japan
| | - Makoto Yamakawa
- Viral Disease and Epidemiology Research Division, NIAH, NARO, Japan
| |
Collapse
|
15
|
Pavón CF, Babadoost M, Lambert KN. Quantification of Phytophthora capsici Oospores in Soil by Sieving-Centrifugation and Real-Time Polymerase Chain Reaction. Plant Dis 2008; 92:143-149. [PMID: 30786362 DOI: 10.1094/pdis-92-1-0143] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
A procedure was developed to quantify Phytophthora capsici oospores in soil by combining a sieving-centrifugation method and a real-time quantitative polymerase chain reaction (QPCR) assay. Five soil samples representing three different soil textures were infested with oospores of P. capsici to produce 101, 102, 103, 104, or 105 spores per 10 g of air-dried soil. Each 10-g sample of infested soil was suspended in 400 ml of water and then passed through 106-, 63-, and 38-μm metal sieves. The filtrate was then passed through a 20-μm mesh filter. Materials caught on the filter were washed with water into two 50-ml centrifuge tubes and spun for 4 min (900 × g). The pellet was suspended in 30 ml of 1.6 M sucrose solution and centrifuged for 45 s (190 × g). The supernatant was passed through the 20-μm mesh filter. The sucrose extraction process of oospores was repeated five times to maximize oospore extraction. Materials caught on the 20-μm mesh filter were washed with water into a 50-ml tube and spun for 4 min (900 × g). The pellet was suspended in 1 ml of water, and the number of oospores was determined with a haemocytometer. The relationship between number of oospores recovered from the soil and number of oospores incorporated into the soil was Ŷ = -0.95 + 1.31X - 0.03X2 (R2 = 0.98), in which Ŷ = log10 of number of oospores recovered from the soil and X = log10 of number of oospores incorporated into the soil. The oospores were germinated after treatment with 0.1% KMnO4 solution for 10 min to induce germination. On the basis of the detection of ribosomal DNA, a QPCR method for P. capsici oospores was developed. PCR inhibitors were eliminated by extracting oospores from the soil by sieving-centrifugation. DNA was extracted and quantified from P. capsici oospores with suspensions of 101, 101.5, 102, 102.5, 103, 103.5, 104, 104.5, and 105 oospores per ml of water. The relationship between the DNA quantities and number of P. capsici oospores was Ŷ = -3.57 - 0.54X + 0.30X2 (R2 = 0.93), in which Ŷ = log10 (nanogram of P. capsici DNA) and X = log10 (number of oospores). The relationship between the quantity of DNA of P. capsici oospores recovered from the soil and the number of oospores incorporated into the soil was determined by Ŷ = -3.53 - 0.73X + 0.32X2 (R2 = 0.955, P < 0.05), in which Ŷ = log10 (DNA quantity of P. capsici oospores recovered from the soil) and X = log10 (number of P. capsici oospores incorporated into the soil). Utilizing the sieving-centrifugation and QPCR methods, oospores of P. capsici were quantified in soil samples collected from commercial fields.
Collapse
Affiliation(s)
- C F Pavón
- Department of Crop Sciences, University of Illinois, Urbana, 61801
| | - M Babadoost
- Department of Crop Sciences, University of Illinois, Urbana, 61801
| | - K N Lambert
- Department of Crop Sciences, University of Illinois, Urbana, 61801
| |
Collapse
|