Journal: Toxics

Article Title: Integrated ceRNA Network Analysis in Silica-Induced Pulmonary Fibrosis and Discovery of miRNA Biomarkers

doi: 10.3390/toxics14010063

Figure Lengend Snippet: Identification of core ncRNAs and genes in key metabolic pathways. ( A ) Core ncRNAs and genes associated with the ECM–receptor interaction pathway, NF-κB signaling pathway, TNF signaling pathway, and PI3K-Akt signaling pathway. ( B ) Validation of expression levels for the core ncRNAs and genes by quantitative real-time PCR ( n = 3, *** p < 0.001 vs. the saline group).

Article Snippet: Amplification and detection were carried out on an Applied Biosystems QuantStudio 3 Real-Time PCR System using the Tiangen SuperReal PreMix Plus (SYBR Green) Kit (Beijing, China) (Cat. Nos.

Techniques: Biomarker Discovery, Expressing, Real-time Polymerase Chain Reaction, Saline

Journal: Microbial Biotechnology

Article Title: Sequential development of several RT‐qPCR tests using LNA nucleotides and dual probe technology to differentiate SARS‐CoV‐2 from influenza A and B

doi: 10.1111/1751-7915.14031

Figure Lengend Snippet: Schematic illustrating SARS‐CoV‐2 genome and regions targeted by RT‐qPCR primers and probes. A. Schematic overview portrays the SARS‐CoV‐2 genome with RdRP and E gene regions magnified to show the locations of primers and probes of the original Charité protocol, vDetect (v1 and v2), and rTEST RT‐qPCR assays. F, forward primer; P, probe; R, reverse primer. The inset boxes (from left to right) illustrate a SARS‐CoV‐2 particle with labelled structural proteins and RNA, legend describing panel A and the primers and probes used in each test to detect RNase P subunit p30 (RPP30). B. Diagram compares the sequences of RdRP and E gene primers and probes for the original Charité protocol, vDetect (v.1) and vDetect v.2 and rTEST RT‐qPCR assays to the Wuhan reference sequence. The numbers written above the Wuhan reference sequence correspond to the start and end base positions of the sequence Reverse primer sequences are written in the reverse complement (rc). Magenta lines and letters represent mixed bases found in the primers and probes in the Charité protocol that were replaced with the correct bases in vDetect v1 (blue lines and letters). Red lines and letters signify LNA‐modified bases.

Article Snippet: RT‐qPCR reactions were optimized on a CFX96 (Bio‐Rad), QuantStudio 5 (Agilent Technologies, CA, USA) and Mx3005P (Agilent Technologies) real time PCR detection systems using the 1Step RT qPCR Probe ROX L Kit (Cat. No. QOP0201, highQu, Germany).

Techniques: Quantitative RT-PCR, Sequencing, Modification

Journal: Microbial Biotechnology

Article Title: Sequential development of several RT‐qPCR tests using LNA nucleotides and dual probe technology to differentiate SARS‐CoV‐2 from influenza A and B

doi: 10.1111/1751-7915.14031

Figure Lengend Snippet: Optimization, analytical sensitivity and clinical performance of a rapid, RNA extraction‐free, multiplexed RT‐qPCR assay. A. Analytical sensitivity of the triplexed E, RdRP and RNase P assay in the rTEST COVID‐19 qPCR Allplex kit. B. Clinical performance of the rTEST COVID‐19 qPCR Allplex kit. C. Optimization of gargle sample input for a rapid, RNA extraction‐free, triplexed rTEST. D. Comparison of four different thermal profiles using 8 μl of gargle input volume in rapid, direct RT‐qPCR. E. Analytical sensitivity of the triplexed E, RdRP and RNase P assay in the RNA extraction‐free rTEST COVID‐19 qPCR Rapid kit. F. Clinical performance of the rTEST COVID‐19 qPCR Rapid kit. The dotted line at C t = 40 (panels A and E) serves as a threshold after which amplification is considered invalid. The dotted lines and shaded areas (panels B and F) indicate samples that were not detected by either the evaluation test, index test or both tests. C t , cycle threshold; E, envelope gene; ND, not detected within 45 cycles; NTC, no template control; RdRP, RNA‐dependent RNA polymerase.

Article Snippet: RT‐qPCR reactions were optimized on a CFX96 (Bio‐Rad), QuantStudio 5 (Agilent Technologies, CA, USA) and Mx3005P (Agilent Technologies) real time PCR detection systems using the 1Step RT qPCR Probe ROX L Kit (Cat. No. QOP0201, highQu, Germany).

Techniques: RNA Extraction, Quantitative RT-PCR, Comparison, Amplification, Control

Journal: Microbial Biotechnology

Article Title: Sequential development of several RT‐qPCR tests using LNA nucleotides and dual probe technology to differentiate SARS‐CoV‐2 from influenza A and B

doi: 10.1111/1751-7915.14031

Figure Lengend Snippet: Schematic illustrating influenza A and B genome and regions targeted by RT‐qPCR primers and probes. (A) Schematic overview portrays the influenza A and B genome with PB1 and PA gene regions magnified to show the locations of primers and probes. Nucleotides labelled in red text indicate mixed bases in the consensus sequences for influenza A and B. BHQ2, black hole quencher 2; F, forward primer; HA, haemagglutinin; M, matrix protein; NA, neuraminidase; NP, nucleoprotein; NS, non‐structural protein; P, probe; PA, polymerase acidic protein; PB1, polymerase basic 1 protein; PB2, polymerase basic 2 protein; R, reverse primer; seg., segment; YY, Yakima Yellow ® .

Article Snippet: RT‐qPCR reactions were optimized on a CFX96 (Bio‐Rad), QuantStudio 5 (Agilent Technologies, CA, USA) and Mx3005P (Agilent Technologies) real time PCR detection systems using the 1Step RT qPCR Probe ROX L Kit (Cat. No. QOP0201, highQu, Germany).

Techniques: Quantitative RT-PCR