Journal: bioRxiv

Article Title: Sorting endosomes play key roles in presentation of Mycobacterium tuberculosis -derived ligands to MAIT cells

doi: 10.64898/2025.12.03.691670

Figure Lengend Snippet: A) RT-qPCR of RNA isolated from Missense control and Stx6 knockdown (KD) BEAS-2Bs. Stx6 expression was calculated relative to Gapdh. B) IFN-γ ELISpot assay with Mtb infected Missense control and Stx6 knockdown BEAS-2Bs using MR1-restricted MAIT cell clone, p=0.7413. MAIT cell responses measured by mean IFN-γ spot forming units (SFU). C) RT-qPCR of RNA isolated from Missense control and Stx12 knockdown BEAS-2Bs. Stx12 expression was calculated relative to Gapdh . D) IFN-γ ELISpot mean SFU from Mtb infected Missense control and Stx12 knockdown BEAS-2Bs using MR1-restricted MAIT cell clone, p=0.0333. E) IFN-γ ELISpot mean SFU from Mtb infected Missense control and Stx12 knockdown BEAS-2Bs using HLA-B45-restricted T cell clone D466-D6, p=0.3375. F) RT-qPCR of RNA isolated from Missense control and Stx16 knockdown BEAS-2Bs. Stx16 expression was calculated relative to Gapdh . G) IFN-γ ELISpot mean SFU from Mtb infected Missense control and Stx16 knockdown BEAS-2Bs using MR1-restricted MAIT cell clone, p<0.0001. H) IFN-γ ELISpot mean SFU from Mtb infected Missense control and Stx16 knockdown BEAS-2Bs using HLA-B45-restricted T cell clone D466-A10, p=0.2345. ELISpot assay data are pooled from n=3 independent experiments. Error bars represent standard error of the mean (SEM). Top and EC 50 SFU values were determined by least-squares regression and used to calculate p-values by extra sum-of-squares F test.

Article Snippet: RT-qPCR was performed using TaqMan Universal PCR Master Mix (Thermo Fisher Scientific) and Taqman FAM-MGB Gene expression Assay probes (Thermo Fisher Scientific) to detect transcripts of Stx6 (Hs01057343_m1), Stx12 (Hs00295291_m1), Stx16 (Hs01002372_m1), MR1 (Hs00155420_m1), and GAPDH (Hs02758991_g1) as an internal reference.

Techniques: Quantitative RT-PCR, Isolation, Control, Knockdown, Expressing, Enzyme-linked Immunospot, Infection

Journal: bioRxiv

Article Title: Sorting endosomes play key roles in presentation of Mycobacterium tuberculosis -derived ligands to MAIT cells

doi: 10.64898/2025.12.03.691670

Figure Lengend Snippet: A) Missense control and B) Stx16 knockdown (KD) BEAS-2B:TET-MR1GFP LV cells stained with antibodies against Stx16 (left) and golgin-97 (center); merge of Stx16 and golgin-97 (right). Representative images from n=2 independent experiments. A single Z-stack is shown. Scale bars represent 10µm. C-D) Sum fluorescence intensity (FI) per cell values from n=2 independent experiments. C) Total FI per cell values of Stx16 staining, p=0.0018. D) Total FI per cell values of golgin-97 staining, p=0.2441. Statistical significance between Missense control and Stx16 knockdown determined using Mann-Whitney test for nonparametric data.

Article Snippet: RT-qPCR was performed using TaqMan Universal PCR Master Mix (Thermo Fisher Scientific) and Taqman FAM-MGB Gene expression Assay probes (Thermo Fisher Scientific) to detect transcripts of Stx6 (Hs01057343_m1), Stx12 (Hs00295291_m1), Stx16 (Hs01002372_m1), MR1 (Hs00155420_m1), and GAPDH (Hs02758991_g1) as an internal reference.

Techniques: Control, Knockdown, Staining, Fluorescence, MANN-WHITNEY

Journal: bioRxiv

Article Title: Sorting endosomes play key roles in presentation of Mycobacterium tuberculosis -derived ligands to MAIT cells

doi: 10.64898/2025.12.03.691670

Figure Lengend Snippet: A) Western blot of Stx16, beta actin, and Stx16-RFP in non-transfected control (NT) and Stx16-RFP transfected BEAS-2B:TET-MR1GFP LV cells. Representative of n=2 independent experiments. B) Stx12-RFP (left) and Stx16-RFP (center) transfected BEAS-2B:TET-MR1GFP LV incubated overnight with doxycycline. Merge of Hoechst, MR1-GFP, and Stx12-RFP or 16-RFP. Representative images from at least n=2 independent experiments. A single Z-stack is shown. Scale bars represent 5µm. Percentage of MR1-GFP Vesicles that co-localize with Stx12-RFP or Stx16-RFP (right). Statistical significance between Stx12-MR1 co-localization and Stx16-MR1 co-localization determined using Mann-Whitney test for nonparametric data, p<0.0001.

Article Snippet: RT-qPCR was performed using TaqMan Universal PCR Master Mix (Thermo Fisher Scientific) and Taqman FAM-MGB Gene expression Assay probes (Thermo Fisher Scientific) to detect transcripts of Stx6 (Hs01057343_m1), Stx12 (Hs00295291_m1), Stx16 (Hs01002372_m1), MR1 (Hs00155420_m1), and GAPDH (Hs02758991_g1) as an internal reference.

Techniques: Western Blot, Transfection, Control, Incubation, MANN-WHITNEY

Journal: bioRxiv

Article Title: Sorting endosomes play key roles in presentation of Mycobacterium tuberculosis -derived ligands to MAIT cells

doi: 10.64898/2025.12.03.691670

Figure Lengend Snippet: A-F) Flow cytometry analyses of 100µM 6-FP or 0.01M NaOH solvent control treated Missense control, Stx12, or Stx16 knockdown (KD) MR1-GFP BEAS-2Bs. Representative histograms (left) and gMFI values (right). A) MR1 surface expression in Missense control and Stx12 knockdown MR1-GFP BEAS-2Bs treated with NaOH solvent control, p=0.0051, or treated with 6-FP, p=0.0002. B) HLA-A,B,C surface expression in Missense control and Stx12 knockdown MR1-GFP BEAS-2Bs treated with NaOH solvent control, p=0.0207, or treated with 6-FP, p=0.0006. C) Total MR1 expression (GFP gMFI) in Missense control and Stx12 knockdown MR1-GFP BEAS-2Bs treated with NaOH solvent control, p=0.0261, or treated with 6-FP, p=0.0091. D) MR1 surface expression in Missense control and Stx16 knockdown MR1-GFP BEAS-2Bs treated with NaOH solvent control, p=0.0020, or treated with 6-FP, p=0.0008. E) HLA-A,B,C surface expression in Missense control and Stx16 knockdown MR1-GFP BEAS-2Bs treated with NaOH solvent control, p=0.0273, or treated with 6-FP, p=0.5967. F) Total MR1 expression (GFP gMFI) in Missense control and Stx16 knockdown MR1-GFP BEAS-2Bs treated with NaOH solvent control, p=0.0068, or treated with 6-FP, p=0.0014. G-I) RT-qPCR of RNA isolated from Missense control, Stx12, and Stx16 knockdown MR1-GFP BEAS-2Bs. Stx12 , Stx16, and MR1 gene expression were calculated relative to Gapdh . Flow cytometry data are pooled from n=4 independent experiments. gMFI values were used to calculate p-values by two-tailed paired t-test.

Article Snippet: RT-qPCR was performed using TaqMan Universal PCR Master Mix (Thermo Fisher Scientific) and Taqman FAM-MGB Gene expression Assay probes (Thermo Fisher Scientific) to detect transcripts of Stx6 (Hs01057343_m1), Stx12 (Hs00295291_m1), Stx16 (Hs01002372_m1), MR1 (Hs00155420_m1), and GAPDH (Hs02758991_g1) as an internal reference.

Techniques: Flow Cytometry, Solvent, Control, Knockdown, Expressing, Quantitative RT-PCR, Isolation, Gene Expression, Two Tailed Test

Journal: Virology

Article Title: Integrated proteomics and transcriptomics analyses identify novel cell surface markers of HIV latency

doi: 10.1016/j.virol.2022.06.003

Figure Lengend Snippet: Antibodies used to test enrichment of latently infected cells from mixed cell populations.

Article Snippet: Antibody Isotype Secondary a Conjugate Manufacturer (cat. #) CEACAM1 Mouse IgG2b N/A PE R&D Systems (FAB2244P) PLXNB1 Mouse IgG2a N/A APC R&D Systems (FAB53291A) STX16 Rabbit IgG Goat anti-Rabbi APC Thermofisher Scientific (PA5-48340) LIMK1 Mouse IgG2b Goat anti-Mouse PE Novus Biologicals (NBP2-00748) LAX1 Rabbit IgG Goat anti-Rabbit APC Abcam (ab133759) ANXA2 Rabbit IgG N/A PE Abcam (ab210729) LGALS1 Mouse IgG1 Goat anti-Mouse PE Thermofisher Scientific (43–7400) EPHA2 Mouse IgG2a N/A APC R&D Systems (FAB3035) CD80 Mouse IgG1 N/A FITC R&D Systems (FAB140F-025) CCL5 Mouse IgG1 N/A APC R&D Systems (IC278A) MX1 Rabbit IgG Goat anti-Rabbit APC Abcam (ab207414) KRAS Mouse IgG2b Goat anti-Mouse PE Novus Biologicals (NBP2-59413) Open in a separate window CEACAM1 , CEA cell adhesion molecule 1; PLXNB2 , plexin B2; STX16 , syntaxin 16; LIMK1 , LIM domain kinase 1; LAX1 , lymphocyte transmembrane adaptor 1; ANXA2 , annexin A2; LGALS1 , galectin 1; EPHA2 , EPH receptor A2; CD80 , CD80 molecule; CCL5 , C─C motif chemokine ligand 5; MX1 , MX dynamin like GTPase 1; KRAS , KRAS proto-oncogene, GTPase; PE, phycoerythrin; APC, allophycocyanin; FITC, fluorescein isothiocyanate; cat. #, catalog number; N/A, not applicable. a Secondary antibody is not applicable for primary antibodies conjugated to fluorophores.

Techniques: Infection

Journal: Virology

Article Title: Integrated proteomics and transcriptomics analyses identify novel cell surface markers of HIV latency

doi: 10.1016/j.virol.2022.06.003

Figure Lengend Snippet: Antibodies used to test enrichment of latently infected cells from mixed cell populations.

Article Snippet: STX16 , Rabbit IgG , Goat anti-Rabbi , APC , Thermofisher Scientific (PA5-48340).

Techniques: Infection