Journal: Genome Research

Article Title: 5?-Transducing SVA retrotransposon groups spread efficiently throughout the human genome

doi: 10.1101/gr.093435.109

Figure Lengend Snippet: Ongoing transcription of SVA_F1 subfamily members is demonstrated by ESTs and RT-PCR analyses. (A) ESTs (arrows) aligning specifically to the source element H10_1 and its descendants (DB277120, AA582071) and to MAST2–SVA junctions of a subset of SVA_F1 subfamily members. Extensions of the queries used to identify ESTs (black bars) are shown. (B) Transcriptional control of transduction group 1 members H20_1 and H1_F_160 is effected by external promoters. Identified ESTs match 5′ junctions of the SVA elements with primary 5′ transductions. MER57A is an internal portion of the nonautonomous retrovirus 1 (ERV1). (C) ESTs indicating ongoing transcription of source element HX_4. Those ESTs that correspond to the 3′-end (BI325030, AW627827) and the 3′ junction (BX110444) of HX_4 are also consistent with transcription of the HX_4 derivative H3_8 (Fig. 7C). 3′-Ends of sense ESTs BI325030 and BX110444 as well as the 5′-end of antisense EST BX373748 are directly at the polyadenylation sites of HX_4 and/or H3_8. SVA copies highlighted in red were verified to be source elements. (D) RT-PCR analyses confirm transcription of distinct SVA_F1 subfamily members. Agarose gel electrophoresis of H20_1 and HX_4/H3_8-specific RT-PCR products derived from total RNA from human tissues and NCCIT cells. Primer binding sites and extension of the RT-PCR products are indicated as short arrows and red bars, respectively, in B and C. To control for both successful cDNA synthesis and DNA-free RNA preparations, PCRs with GAPDH-specific, intron-spanning primers (see Methods) were performed on RNA preparations from each tissue before (−RT) and after (+RT) cDNA synthesis. PCR on genomic HeLa DNA served as a positive control. The 766- and 481-bp products originate from the unspliced GAPDH gene and a processed GAPDH pseudogene, respectively (Harper et al. 2003). Sizes of obtained PCR products are indicated and correspond to expected fragment sizes. RT, reverse transcriptase; M, size marker; NTC, no template control.

Article Snippet: Total RNA was extracted from human teratocarcinoma cell line NCCIT (ATCC CRL-2073) using TRIzol reagent (Invitrogen).

Techniques: Reverse Transcription Polymerase Chain Reaction, Transduction, Agarose Gel Electrophoresis, Derivative Assay, Binding Assay, Positive Control, Marker

Journal: Scientific Reports

Article Title: Translational feasibility and efficacy of nasal photodynamic disinfection of SARS-CoV-2

doi: 10.1038/s41598-022-18513-0

Figure Lengend Snippet: aPDT response in HCoV-OC43 inoculum. ( A ) RT-PCR analysis, showing the reduction in viral RNA copies per μl of total extracted RNA as a function of MB photosensitizer concentration for different light doses (coloured lines). ( B ) Corresponding infectivity measurements expressed as median tissue culture infection dose (TCID 50 ). Data points are mean ± 1 standard deviation for n = 3–6 replicates. All aPDT protocols demonstrated significantly reduced viral RNA copies/μl and TCID compared to controls (light only, MB only, and no treatment groups, P < 0.05).

Article Snippet: To quantify viral copy number, standard curves were generated using SARS-CoV-2 or HCoV-OC43 synthetic RNA standards (Twist Biosci).

Techniques: Reverse Transcription Polymerase Chain Reaction, Concentration Assay, Infection, Standard Deviation

Journal: Viruses

Article Title: Evaluation of a Lyophilized CRISPR-Cas12 Assay for a Sensitive, Specific, and Rapid Detection of SARS-CoV-2

doi: 10.3390/v13030420

Figure Lengend Snippet: Cross-reaction evaluation of Lyo-CRISPR SARS-CoV-2 kit with other respiratory pathogens.

Article Snippet: Respiratory syncytial virus , ATCC ® VR-1580DQ , 10 5 copies/mL , 0/3 , Negative , 3/3 , Valid.

Techniques: Concentration Assay