Journal: STAR Protocols

Article Title: qRT-PCR Platforms for Diagnosing and Reporting SARS-CoV-2 Infection in Human Samples

doi: 10.1016/j.xpro.2020.100102

Figure Lengend Snippet: Appropriate and Inappropriate qRT-PCR Curves for Samples (A) Representation of curves for N1 gene in one patient sample. Each curve represents one technical replicate (i.e., one well) of the qRT-PCR run. The curve labeled with an asterisk (∗) denotes what one would expect if N1 transcript is not present in the sample. The curve labeled with yellow arrow head represents a spurious curve with a C T value of 5.594 likely due to technical artifact. (B) Technical duplicate curves generated for N1 gene in one positive patient sample. These curves, with C T value of 31.131, are what one would expect if the qRT-PCR run identified SARS-CoV-2 viral genomic RNA present in patient samples.

Article Snippet: Please note however, that it is possible to obtain full-length SARS-CoV-2 genomic RNA from ATCC (Cat. No. VR-1986D) to use in lieu of or addition to the TaqPath COVID-19 Combo Kit positive control.

Techniques: Quantitative RT-PCR, Labeling, Generated

Journal: STAR Protocols

Article Title: qRT-PCR Platforms for Diagnosing and Reporting SARS-CoV-2 Infection in Human Samples

doi: 10.1016/j.xpro.2020.100102

Figure Lengend Snippet:

Article Snippet: Please note however, that it is possible to obtain full-length SARS-CoV-2 genomic RNA from ATCC (Cat. No. VR-1986D) to use in lieu of or addition to the TaqPath COVID-19 Combo Kit positive control.

Techniques: Reverse Transcription, Adhesive, Multiplex Assay, Software, Real-time Polymerase Chain Reaction

Journal: Current biology : CB

Article Title: A conserved PDZ Binding Motif in aPKC interacts with Par-3 and mediates cortical polarity

doi: 10.1016/j.cub.2019.12.055

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: Doe Lab N/A D. melanogaster: elav-Gal4, UAS-mCD8:GFP, hs:flp; FRT-G13, tubPGal80 Bloomington Drosophila Stock Center RRID:BDSC_5145 Oligonucleotides Recombinant DNA pCMV mammalian expression plasmid ThermoFisher 10586014 pMal C4X bacterial expression plasmid Addgene 75288 pGex 4Ti bacterial expression plasmid Amersham 27458001 pUASTattB fly cloning and transformation plasmid Addgene EF362409.1 Software and Algorithms ImageJ GraphPad Other PD10 Desalting columns 95017–001 VivaSpin 20 sample concentrators MWCO 30kD VWR 95056–130 VivaSpin 20 sample concentrators MWCO 10kD VWR 95056–128 Shaker Flasks – 125mL VWR 89095–258 Open in a separate window KEY RESOURCES TABLE Par-3 and Par-6/aPKC interact through a PDZ2 – PDZ Binding Motif interaction The Par-3 PDZ2 interaction with the aPKC PBM is conserved across metazoan The aPKC PBM is required for cortical polarity in Drosophila neuroblasts

Techniques: Diagnostic Assay, Recombinant, Construct, Variant Assay, Expressing, Blocking Assay, Plasmid Preparation, Clone Assay, Transformation Assay, Software

Journal: NPJ Vaccines

Article Title: Immunization-induced antigen archiving enhances local memory CD8+ T cell responses following an unrelated viral infection

doi: 10.1038/s41541-024-00856-6

Figure Lengend Snippet: a Experimental schematic for b – e . C57/BL6 mice were immunized subcutaneously in the footpad and/or flank with the indicated antigens and adjuvants. b Cells were stained with CD45, PDPN, CD31 and PD-L1. Cells were gated on CD45-PDPN + CD31- for FRC and CD45-PDPN + CD31+ for LECs. Shown are examples of LEC and FRC antigen-positive cells based on PD-L1 expression (floor, MARCO LEC) and ova-AF488+ from mice 2–3 weeks after immunization with ova conjugated to Alexa-Fluor 488 (AF488) and polyI:C and αCD40. c Quantification of the frequency of LEC, BEC, and FRC in the popliteal lymph node (pLN) that are positive for the indicated antigens administered with polyI:C and αCD40 at indicated time. d Same as ( b ) except for mice were immunized with SARS-CoV-2-RBD-AF488, polyI:C, and αCD40. e Same as in ( c ) except for SARS-CoV-2-RBD and CHIKV-E2 with polyI:C and αCD40. CHIKV-E2 was repeated for 9–14 days post-vaccine (~2 weeks). Statistical analysis was done using an unpaired t -test where the p -value between naïve and indicated antigen is <0.0001. In each experiment, at least n = 2–3 mice per group were evaluated and the experiment was repeated n = 2–5 times for c – e . Shown is the representative data from one of the experiments. Error bars are mean ± standard error of the mean. ns not significant, * p < 0.05, ** p < 0.01, *** p < 0.001, **** p < 0.0001.

Article Snippet: Ova (10 μg) was purchased from Sigma-Aldrich (Cat No. A5503) and Chikungunya virus envelope 2 protein (8 μg) (CHIKV-E2, strain SL-CK1) was purchased from Sino Biological (Cat. No. 40440-V08B).

Techniques: Staining, Expressing

Journal: iScience

Article Title: 5-Hydroxymethyltubercidin exhibits potent antiviral activity against flaviviruses and coronaviruses, including SARS-CoV-2

doi: 10.1016/j.isci.2021.103120

Figure Lengend Snippet:

Article Snippet: Recombinant ZIKV NS5 protein , Sino Biological , Cat# 40546-V08B.

Techniques: Virus, Recombinant, Software, Real-time Polymerase Chain Reaction, Fluorescence, Microscopy

Journal: Emerging Microbes & Infections

Article Title: A pan-orthoebolavirus neutralizing antibody encoded by mRNA effectively prevents virus infection

doi: 10.1080/22221751.2024.2432366

Figure Lengend Snippet: The mAb 2G1 exhibited a broad anti-orthoebolaviruses activity. (A) Recognition of 2G1 to the full length of orthoebolavirus GPs displayed on the cell surface. Data represent mean ± SD of three replicates from one representative experiment. An FITC-labeled irrelevant mAb was used as the control. (B) Binding kinetics of 2G1 to EBOV GPΔTM or GPΔMuc determined by surface plasmon resonance. Five representative curves from one representative test were fitted to compute the kinetic constants. (C) Binding activities of 2G1 to EBOV GPΔTM, GPΔMuc, and GPcl under various pH conditions tested by ELISA. (D) Neutralization capacities of 2G1, FVM04, and mAb114 against pseudotyped rHIV-EBOV (Makona), – EBOV (Mayinga), – SUDV, – BDBV, – TAFV, and – RESTV. Data are presented as the mean ± SD of three replicates from one representative experiment. (E) The amino acid divergence between the original and inferred genes of 2G1. (F) The binding abilities of the wild-type and inferred germline cross-pairing forms of 2G1 to EBOV GPΔMuc, tested by ELISA. (G) The binding curves of HCDR mutants of 2G1 to EBOV GPΔMuc.

Article Snippet: Recombinant EBOV GPΔTM was purchased from Sino Biological Inc. (Beijing, China; Cat No. 40442-V08H4).

Techniques: Activity Assay, Labeling, Control, Binding Assay, SPR Assay, Enzyme-linked Immunosorbent Assay, Neutralization

Journal: Emerging Microbes & Infections

Article Title: A pan-orthoebolavirus neutralizing antibody encoded by mRNA effectively prevents virus infection

doi: 10.1080/22221751.2024.2432366

Figure Lengend Snippet: 2G1 recognized the hydrophobic pocket beneath the N-terminal tail of GP2 and inhibited GP proteolysis. (A) Front and top views of the cryo-EM structure of the EBOV GPΔMuc/2G1 Fab complex. Molecules are shown as surface representations. The GP1/2 subunits of three protomers A – C of GPΔMuc are colored in pale/blue violet, light/dodger blue, and light/hot pink, respectively. The VH of 2G1 is colored in lime green, and the VL is colored in goldenrod. (B) Superimposition of the 2G1, KZ52 (PDB ID: 5HJ3), and ADI-15878 (PDB ID: 6EA7) variable regions onto EBOV GPΔMuc. Molecules are shown as surface representations. 2G1, KZ52, and ADI-15878 were colored goldenrod, light sea green, and lime green, respectively. (C) Footprints of 2G1 or ADI-15878 on the EBOV GPΔMuc. The buried areas of 2G1 and ADI-15878 are indicated by goldenrod and lime green dotted lines, respectively. The paratope residues of 2G1 are shown as sticks. (D) Magnified view of the interface between 2G1 and EBOV GPΔMuc. EBOV GPΔMuc is represented as a molecular surface, the interface residues are shown as stick representations, and H-bonds are indicated by dotted black lines. GP1 (protomer A), GP2 (protomer A), GP2 (protomer B), 2G1 HCDR, 2G1 LCDR, oxygen atoms, and nitrogen atoms are colored pale violet, blue violet, dodger blue, lime green, goldenrod, red, and blue, respectively. (E) Relative binding percentage (%WT) of non-competing 2G1 and 4F1 to surface-anchored EBOV GP mutants. Data represent the means of three replicates of one representative experiment. Minor and pivotal epitopes of 2G1 are indicated in orange and dodger blue, respectively. (F) Conservation of critical 2G1 epitopes among filovirus GPs. (G) Antibodies blocking the binding of NPC1-C to GPcl. (H) Ability of antibodies or Fabs to inhibit the cleavage of EBOV GPΔMuc by thermolysin. THL, thermolysin; IMF, intermediate mass fragment.

Article Snippet: Recombinant EBOV GPΔTM was purchased from Sino Biological Inc. (Beijing, China; Cat No. 40442-V08H4).

Techniques: Cryo-EM Sample Prep, Binding Assay, Blocking Assay

Journal: Emerging Microbes & Infections

Article Title: A pan-orthoebolavirus neutralizing antibody encoded by mRNA effectively prevents virus infection

doi: 10.1080/22221751.2024.2432366

Figure Lengend Snippet: mRNA-2G1-LNP potently inhibited the pseudotyped EBOV and SUDV infection. (A) The neutralization ability of mRNA-2G1-LNP against rHIV-EBOV. (B and C) The in vivo protection efficacy of mRNA-2G1-LNP against rHIV-EBOV in mice. The normalized bioluminescence intensity (p/s/cm2/sr) of images captured four days post-infection (B) was calculated and compared to the PBS group (C). (D – F) In vitro neutralization ability (D) and in vivo protective efficacy (E and F) of mRNA-2G1-LNP against rHIV-SUDV. (G) Serum antibody concentration. BALB/c mice ( n = 5) were administered a single dose of mRNA-2G1-LNP, 2G1 antibody, or an equal volume of empty LNP. Antibody concentrations at the indicated times were determined using quantitative ELISA. (I – L) Comparison of biochemical criteria in the serum three days post-administration between the mRNA-2G1-LNP (1 mg/kg) and PBS groups. ALT, alanine aminotransferase; AST, aspartate aminotransferase; LDH, lactate dehydrogenase; CR, creatinine.

Article Snippet: Recombinant EBOV GPΔTM was purchased from Sino Biological Inc. (Beijing, China; Cat No. 40442-V08H4).

Techniques: Infection, Neutralization, In Vivo, In Vitro, Concentration Assay, Enzyme-linked Immunosorbent Assay, Comparison

Journal: iScience

Article Title: Compartment-specific antibody correlates of protection to SARS-CoV-2 Omicron in macaques

doi: 10.1016/j.isci.2024.110174

Figure Lengend Snippet:

Article Snippet: SARS-CoV-2 Ebola Glycoprotein , Sino Biological , 40459-V08H.

Techniques: Recombinant, Isolation, Cell Isolation, Chromatography, Software, Luminex

Journal: Cell host & microbe

Article Title: Longitudinal human antibody repertoire against complete viral proteome from Ebola virus survivor reveals protective sites for vaccine design

doi: 10.1016/j.chom.2020.01.001

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: Zaire EBOV VP40 Matrix protein , Sino Biologicals , 40446-V07E.

Techniques: Recombinant