Journal: medRxiv

Article Title: Clinical validation of a novel metagenomic nanopore sequencing method for detecting viral respiratory pathogens

doi: 10.64898/2026.02.06.26345651

Figure Lengend Snippet: Red indicates passed and black failed. RNA from murine respirovirus, orthoreovirus and Zika virus were spiked as cDNA synthesis and SISPA controls, MS2 phage was spiked as an extraction, cDNA synthesis and SISPA control. Within the derivation set MS2 was not required to pass QC due to poor performance of the laboratory MS2 stock; in both validation and derivation only detection of 2/3 virus spikes was required to pass QC.

Article Snippet: Extracted RNA (8μl) was treated with DNAse, as recommended, then spiked with three reverse transcription/amplification controls (1μl each, containing approximately 10 4 genome copies each of Zika virus (ATCC-VR-1838DQ), murine respirovirus (ATCC-VR-907DQ) and orthoreovirus (ATCC-VR-824DQ) (ATCC Manassas, Virginia, USA). cDNA synthesis was primed randomly using the 3’ terminal N 9 segment of custom oligonucleotide primers (5’-GAT-GAT-AGT-AGG-GCT-TCG-TCA-CNN-NNN-NNN N-3’; Integrated DNA Technologies, Leuven, Belgium), final concentration 5μM.

Techniques: Virus, cDNA Synthesis, Extraction, Control, Biomarker Discovery

Journal: Cell metabolism

Article Title: Deamidation Shunts RelA from Mediating Inflammation to Aerobic Glycolysis

doi: 10.1016/j.cmet.2020.04.006

Figure Lengend Snippet: (A) NF-κB luciferase reporter assay from 293T cells with shRNA targeting indicated cellular glutamine amidotransferases upon Sendai virus (SeV) infection. CTPS: CTP synthetase; PFAS: phosphoribosylformylglycinamidine synthetase; GMPS: GMP synthetase; GFPT: glutamine fructose-6-phosphate amidotransferase; ASNS: Asparagine synthetase; NADSYN1: NAD synthetase 1; CPS1: carbamoyl-phosphate synthetase; and PPAT: phosphoribosyl pyrophosphate amidotransferase. CAD, please see text.

Article Snippet: Microbes Sendai virus (Cantell strain) was purchased from Charles River.

Techniques: Luciferase, Reporter Assay, shRNA, Virus, Infection

Journal: Proceedings of the National Academy of Sciences of the United States of America

Article Title: Mitochondrial-associated endoplasmic reticulum membranes (MAM) form innate immune synapses and are targeted by hepatitis C virus

doi: 10.1073/pnas.1110133108

Figure Lengend Snippet: The MAM is an innate immune signaling platform. (A and B) Immunoblot analysis of fractionated Huh7 (−) and Huh7-HCV K2040 (+) cells. Arrows indicate full-length (FL) and cleaved (C) MAVS. (C) Immunoblot analysis of fractions immunoprecipitated with anti–RIG-I from mock- or SenV-infected (for 8 h) PH5CH8 cells and input. *Nonspecific band. Fractionation markers: calnexin, ER; Cox-1, mitochondria; FACL4, MAM; tubulin, cytosol; Pex19, peroxisomes.

Article Snippet: SenV strain Cantell was obtained from Charles River Laboratory.

Techniques: Western Blot, Immunoprecipitation, Infection, Fractionation

Journal: Proceedings of the National Academy of Sciences of the United States of America

Article Title: Mitochondrial-associated endoplasmic reticulum membranes (MAM) form innate immune synapses and are targeted by hepatitis C virus

doi: 10.1073/pnas.1110133108

Figure Lengend Snippet: Mitochondrial–ER contacts regulate RIG-I pathway antiviral signaling. (A and B) Immunoblot analysis and IFN-β promoter luciferase expression of Huh7 cells treated with nontargeting control (CTRL), MFN1, or MFN2 siRNA pools or methyl-β cyclodextrin and then mock- or SenV-infected. Values are mean ± SD (n = 3) of one of three representative experiments. *P ≤ 0.05; **P ≤0.005; ***P ≤0.0005, by unpaired Student t test. (C) HCV copy number (mean ± SD; n = 3). (Inset) Immunoblot analysis of MAVS; full-length (FL) and cleaved (C). (D) (Upper) HCV-positive cells after 72 h of infection (mean ± SD; n = 5–6). (Lower) Percent VSV-positive cells after 16 h of VSV infection (mean ± SD; n = 3–5, >1000+ cells counted). (E and F) Confocal micrographs of immunostained SenV-infected Huh7 cells expressing mEGFP-PSS-1 (MAM) (E) or HCV NS4A-mEGFP (F) with PMP70 (peroxisomes) and TOM20 (OMM) and 3D reconstruction of Z stacks. Arrows mark synapses. Single-cell images are representative of two experiments and >10 cells analyzed per experiment. (Scale bar: 10 μm.)

Article Snippet: SenV strain Cantell was obtained from Charles River Laboratory.

Techniques: Western Blot, Luciferase, Expressing, Control, Infection