Journal: Microbiology Spectrum

Article Title: Development and validation of genome-informed and multigene-based qPCR and LAMP assays for accurate detection of Dickeya solani : a critical quarantine pathogen threatening the potato industry

doi: 10.1128/spectrum.00784-24

Figure Lengend Snippet: Standard curves and graphs for TaqMan-qPCR generated using ten-fold serial diluted Dickeya solani genomic DNA (10 ng to one fg). ( A and C ) Multiplex TaqMan-qPCR, ( D and E ) Single TaqMan-qPCR with 10-fold serially diluted genomic DNA; and ( B ) Multiplex TaqMan qPCR 10-fold serially diluted genomic DNA mixed with host plant DNA. The orange, green, yellow and crimson channels correspond to the different reported dyes Red –BHQ2, 6-FAM (495/520), HEX (535/554), and Quasar705-IBQ3 (excitation/emission spectra in nm), respectively. A1/A2/A3/A4-multiplex TaqMan qPCR generated by multiplexing Dso-wF1/wR1/Dso-P1, Dso-wF2/wR2/Dso-P2, DICg-wF1/wR1/DICg-P, and UIC-wF/wR/UIC-P primer/probe sets. B1/B2/B3/B4-spiked multiplex TaqMan qPCR generated by multiplexing Dso-wF1/wR1/Dso-P1, Dso-wF2/wR2/Dso-P2, DICg-wF1/wR1/DICgP, UIC-wF/wR/ UIC-P primer/probe sets; the spiked assay was done by adding 1 µL of healthy potato DNA extracted from tubers to each 10-fold serially diluted D. solani DNA. C1/C2/C3-multiplex TaqMan qPCR was generated by multiplexing Dso-wF1/wR1/Dso-P1, Dso-wF2/wR2/Dso-P2, and DICg-wF1/wR1/DICg-P primer/probe sets. (D) Single TaqMan qPCR with Dso-wF1/wR1/Dso-P1 primer set in the reaction mix. (E) Single TaqMan qPCR with Dso-wF2/wR2/Dso-P2 probe and primer set. X axis represents the number of cycles, and Y axis-normalized fluorescence. The C T values are average of three replicates ±SD. Slopes (Y = threshold cycles (Ct) of target DNA detected), R 2 (correlation coefficient), and E (amplification efficiency).

Article Snippet: In first lab [Phytobacteriology Lab, Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, HI, USA] LAMP and multiplex qPCR assays were performed in Rotor-Gene Q thermocycler (Biorad) by one operator, while in the second laboratory [Plant Pathogen Confirmatory Diagnostics in Laurel MD (APHIS PPQ S&T), USA] another operator used- Genei III (Optigene, West Sussex, UK) and Mic qPCR Cycler (Bio Molecular Systems, NSW, Australia) for performing LAMP and multiplex qPCR assay, respectively.

Techniques: Generated, Multiplex Assay, Multiplexing, Fluorescence, Amplification

Journal: Microbiology Spectrum

Article Title: Development and validation of genome-informed and multigene-based qPCR and LAMP assays for accurate detection of Dickeya solani : a critical quarantine pathogen threatening the potato industry

doi: 10.1128/spectrum.00784-24

Figure Lengend Snippet: Multi-laboratory validation of loop-mediated isothermal amplification (LAMP) and TaqMan qPCR for specific detection of Dickeya solani .

Article Snippet: In first lab [Phytobacteriology Lab, Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, HI, USA] LAMP and multiplex qPCR assays were performed in Rotor-Gene Q thermocycler (Biorad) by one operator, while in the second laboratory [Plant Pathogen Confirmatory Diagnostics in Laurel MD (APHIS PPQ S&T), USA] another operator used- Genei III (Optigene, West Sussex, UK) and Mic qPCR Cycler (Bio Molecular Systems, NSW, Australia) for performing LAMP and multiplex qPCR assay, respectively.

Techniques: Amplification

Journal: Frontiers in Medicine

Article Title: ACE2 and TMPRSS2 genetic polymorphisms as potential predictors of COVID−19 severity and outcome in females

doi: 10.3389/fmed.2024.1493815

Figure Lengend Snippet: TMPRSS2 frequency of allele and genotype groups in male and female according to outcome of SARS-CoV-2 infection.

Article Snippet: Genotyping for ACE2 and TMPRSS2 gene polymorphisms was performed on Mic qPCR 48-well thermal cycler (BioMolecular Systems) using predesigned, commercially available TaqMan genotyping assay mix (20X; C__16098179_20 for rs2106809; C__16163821_10 for rs2074192; C___2592038_1_ for rs2070788 and C___3080270_20 for rs4818239; Applied Biosystems, Foster City, United States).

Techniques: Infection

Journal: Frontiers in Medicine

Article Title: ACE2 and TMPRSS2 genetic polymorphisms as potential predictors of COVID−19 severity and outcome in females

doi: 10.3389/fmed.2024.1493815

Figure Lengend Snippet: TMPRSS2 frequency of allele and genotype groups in male and female according severity of SARS-CoV-2 infection.

Article Snippet: Genotyping for ACE2 and TMPRSS2 gene polymorphisms was performed on Mic qPCR 48-well thermal cycler (BioMolecular Systems) using predesigned, commercially available TaqMan genotyping assay mix (20X; C__16098179_20 for rs2106809; C__16163821_10 for rs2074192; C___2592038_1_ for rs2070788 and C___3080270_20 for rs4818239; Applied Biosystems, Foster City, United States).

Techniques: Infection

Journal: Frontiers in Medicine

Article Title: ACE2 and TMPRSS2 genetic polymorphisms as potential predictors of COVID−19 severity and outcome in females

doi: 10.3389/fmed.2024.1493815

Figure Lengend Snippet: Summary of variable estimates from the best fitting models of multiple logistic regression analysis regarding severity and outcome of SARS-CoV-2 infection in females.

Article Snippet: Genotyping for ACE2 and TMPRSS2 gene polymorphisms was performed on Mic qPCR 48-well thermal cycler (BioMolecular Systems) using predesigned, commercially available TaqMan genotyping assay mix (20X; C__16098179_20 for rs2106809; C__16163821_10 for rs2074192; C___2592038_1_ for rs2070788 and C___3080270_20 for rs4818239; Applied Biosystems, Foster City, United States).

Techniques: Infection