Journal: medRxiv

Article Title: Association of circulating Fibroblast Growth Factor-2 with progression of HIV-chronic kidney diseases in children

doi: 10.1101/2020.12.08.20246280

Figure Lengend Snippet: Panels A and B, show representative pictures of human monocytes-macrophages treated with either PBS (A) or hr-FGF-2 (20 ng/ml) for three days (B). Scale bars, 100 μm. Panels C and D show representative pictures of syncytia formation in HIV-infected peripheral blood mononuclear cells seeded on fibrin gels derived from plasma taken from a child with a high viral load, and exposed for five days to either PBS (C) or FGF-2 (20 ng/ml). Scale bars, 50μm. Panel E shows cultured human macrophages stained red with an antibody against the CD-68 antigen. Panel F shows a co-localized HIV-RNA staining (blue color by in situ hybridization) and CD-68 staining (red color by immunohistochemistry) in HIV-infected mononuclear cells. Scale bars, 25μm. The graphs, in panels G and H, show the quantitative scores corresponding to the attachment of monocyte-macrophage and their ability to form syncytia (n = 6 samples per group). The Error bars in the graphs reflect the 95% CI. *P < 0.05 were considered statistically significant by the Mann-Whitney test.

Article Snippet: The HIV in situ hybridization studies were done using an HIV-probe from Lofstrand Labs Ltc. (Gaithersburg, MD, USA) as described before.

Techniques: Infection, Derivative Assay, Cell Culture, Staining, In Situ Hybridization, Immunohistochemistry, MANN-WHITNEY

Journal: BMC Developmental Biology

Article Title: BMP-SMAD signalling output is highly regionalized in cardiovascular and lymphatic endothelial networks

doi: 10.1186/s12861-016-0133-x

Figure Lengend Snippet: The GFP reporter protein faithfully recapitulates the transcriptional activation of the BRE :: gfp transgene. In situ hybridisation for gfp mRNA ( red ) and direct GFP fluorescence ( green ) on cryosections through the cardinal vein ( a – d ) and the ventricular trabeculae ( e – g ) at E11.5. DAPI is used to stain nuclei. The boxed area in ( a ) is enlarged in panels ( b – d ). The corresponding low magnification view of the trabeculae in the ventricle is not provided because of insufficient intensity of the ISH signal. White arrowheads indicate ECs double positive for gfp mRNA and direct GFP fluorescence. The red and green arrows depict ECs only positive for gfp mRNA or GFP fluorescence respectively. Scale bars: 100 μm ( a ); 50 μm ( b – d ); 10 μm ( e – g )

Article Snippet: The GFP fluorescent in situ hybridisation (ISH) probe was custom designed with the probe designer tool from Stellaris (LGC biosearch technologies).

Techniques: Activation Assay, In Situ, Hybridization, Fluorescence, Staining

Journal: Annals of epidemiology

Article Title: Associations between County-level Voter Turnout, County-level Felony Voter Disenfranchisement, and Sexually Transmitted Infections among Women in the Southern United States

doi: 10.1016/j.annepidem.2018.10.006

Figure Lengend Snippet:

Article Snippet: STI Specimen Type Alabama Florida Test (Sensitivity, Specificity) by Site Georgia North Carolina Mississippi Chlamydia Cervical swab 1 APTIMA Nucleic Acid Amplification Test (NAAT) (94.30, 98.00) Becton Dickinson (BD) Probetec ET System (93.80, 99.80) Aptima Combo 2 for CT/NG (96.60, 98.50) Gen Probe Aptima (98.30, 96.10) ROCHE Cobas polymerase chain reaction (PCR) (94.90, 99.40) Gonorrhea Cervical swab 1 APTIMA NAAT (92.00, 99.80) BD Probetec ET System (88.00, 99.80) Aptima Combo 2 for CT/NG (96.60, 98.50) Gen Probe Aptima (97.30, 99.00) ROCHE Cobas PCR (96.60, 99.90 Trichomoniasis Vaginal swab 2 APTIMA NAAT (100.00, 98.10) Wet mount 3 (N/A) Wet mount 3 (N/A) Wet mount 3 (N/A) Wet mount 3 (N/A) Early Syphilis 4 Serum BD Screening rapid plasma regain (RPR) with confirmatory Treponema pallidum haemagglutination assay or Treponema pallidum particle agglutination assay (Screening: 3.00- 100.00, 98.00, Confirmatory: 99.40, 100.00) Arlington Scientific RPR Card (95.00, 98.00) BD RPR titer, with confirmatory IgG enzyme immunoassay if reactive (N/A) Labcorp Screening RPR with Confirmatory Quantitative RPR (Screening: 99.00, 98.40; Confirmatory: 100.00, 99.80) BD RPR (86.00, N/A) Open in a separate window 1 Urine was used for testing at Alabama site.

Techniques: Amplification, Polymerase Chain Reaction, Clinical Proteomics, Treponema Pallidum Haemagglutination Assay, Agglutination, Enzyme-linked Immunosorbent Assay

Journal: Cell Death & Disease

Article Title: LINC01106 post-transcriptionally regulates ELK3 and HOXD8 to promote bladder cancer progression

doi: 10.1038/s41419-020-03236-9

Figure Lengend Snippet: a The relative expression of LINC01116 was analyzed in patients with different stages of BCa tissues using the GEPIA 2 bioinformatics website. b The overall survival rate was detected by GEPIA 2 bioinformatics website. c RT-qPCR was used to detect the expression of LINC01116 in human bladder epithelial immortalized cell line SV-HUC-1 and human BCa cell lines (RT-4, 5637, J82, and T24). d RT-qPCR analysis detected LINC01116 expression in J82 and T24 cells transfected with shRNAs targeting LINC01116. e , f Colony formation assay, and EdU assay tested whether LINC01116 knockdown affects the proliferation ability of BCa cell lines. g , h JC-1 assay, and flow cytometry analysis revealed the apoptosis rate of J28 and T24 cells transfected with shRNAs targeting LINC01116. i , j Tumor volume, and tumor weight were measured in response to LINC01116 knockdown. k IHC assay detected the staining of Ki67 and PCNA in tumors with or without LINC01116 knockdown. * P < 0.05, ** P < 0.01.

Article Snippet: The fixed J82 and T24 cells were rinsed in PBS, dehydrated, and air-dried for cultivating in hybridization buffer with LINC01116-specific RNA fluorescence in situ hybridization (FISH) probe (Ribobio).

Techniques: Expressing, Quantitative RT-PCR, Transfection, Colony Assay, EdU Assay, Flow Cytometry, Staining

Journal: Cell Death & Disease

Article Title: LINC01106 post-transcriptionally regulates ELK3 and HOXD8 to promote bladder cancer progression

doi: 10.1038/s41419-020-03236-9

Figure Lengend Snippet: a , b Transwell assays were performed to explore the role of LINC01116 knockdown in BCa cells migration and invasion. c E-cadherin, Vimentin, and N-cadherin expression were measured by western blot in J82 and T24 cells transfected with sh-LINC01116#1 and sh-LINC01116#2. d IF assay determined the staining of E-cadherin and N-cadherin in J82 and T24 cells with or without LINC01116 silence. e The representative image of lungs from the two groups, and HE staining of metastasis nodules in these lungs. * P < 0.05, ** P < 0.01.

Article Snippet: The fixed J82 and T24 cells were rinsed in PBS, dehydrated, and air-dried for cultivating in hybridization buffer with LINC01116-specific RNA fluorescence in situ hybridization (FISH) probe (Ribobio).

Techniques: Migration, Expressing, Western Blot, Transfection, Staining

Journal: Cell Death & Disease

Article Title: LINC01106 post-transcriptionally regulates ELK3 and HOXD8 to promote bladder cancer progression

doi: 10.1038/s41419-020-03236-9

Figure Lengend Snippet: a , b . Nuclear separation followed by RT-qPCR and AGE, as well as FISH assay, monitored the subcellular location of LINC01116 in BCa cells. c , d GEPIA 2 analyzed the relationship between two protein-coding genes (ELK3 and HOXD8) and LINC01116 in BLCA tumors. e , f RT-qPCR and western blot analyzed the expression of ELK3 in BCa cells under LINC01116 inhibition. g , h RT-qPCR and western blot analyzed the expression of HOXD8 in BCa cells. i , j Dual-luciferase reporter assay further validated the combination between ELK3/HOXD8 and LINC01116. * P < 0.05, ** P < 0.01.

Article Snippet: The fixed J82 and T24 cells were rinsed in PBS, dehydrated, and air-dried for cultivating in hybridization buffer with LINC01116-specific RNA fluorescence in situ hybridization (FISH) probe (Ribobio).

Techniques: Quantitative RT-PCR, Western Blot, Expressing, Inhibition, Luciferase, Reporter Assay

Journal: Cell Death & Disease

Article Title: LINC01106 post-transcriptionally regulates ELK3 and HOXD8 to promote bladder cancer progression

doi: 10.1038/s41419-020-03236-9

Figure Lengend Snippet: a Ago2-RIP assay was performed to prove the existence of LINC01116 and ELK3 in RISCs. b , c By means of searching on starBase, miR-3612 was predicted to have the potentials to bind with LINC01116 andELK3. d , e Luciferase reporter gene assays predicted the relationship between miR-3612 and LINC01116/ELK3. f RNA pull-down assay further examined the combination between miR-3612 and LINC01116/ELK3. g Ago2-RIP assay confirmed the interaction among LINC01116, miR-3612, and ELK3 in RISCs. h RNA pull-down assay detected the impact of LINC01116 on the interaction of miR-3612 with ELK3. * P < 0.05, ** P < 0.01.

Article Snippet: The fixed J82 and T24 cells were rinsed in PBS, dehydrated, and air-dried for cultivating in hybridization buffer with LINC01116-specific RNA fluorescence in situ hybridization (FISH) probe (Ribobio).

Techniques: Luciferase, Pull Down Assay

Journal: Cell Death & Disease

Article Title: LINC01106 post-transcriptionally regulates ELK3 and HOXD8 to promote bladder cancer progression

doi: 10.1038/s41419-020-03236-9

Figure Lengend Snippet: a StarBase software predicted thirteen RBPs shared between HOXD8 and LINC01116. b RT-qPCR detected the relative expression of HOXD8 in J28 cells transfected with shRNAs targeting indicated RBPs. c RNA pull-down assay tested the interaction of LINC01116 with DKC1 or ELACL1. d RNA pull-down assay detected the interaction between HOXD8 and DKC1. e RIP assay verified whether LINC01116 or HOXD8 could be enriched in the anti-DKC1 pallet. f , g RT-qPCR analysis, and western blot analyzed that the expression of DKC1/HOXD8 in J82 and T24 cells transfected with shRNAs against DKC1. h RT-qPCR examined the stability of HOXD8 under ActD treatment in J82 and T24 cells transfected sh-LINC01116#1 or sh-DKC1#1. * P < 0.05, ** P < 0.01.

Article Snippet: The fixed J82 and T24 cells were rinsed in PBS, dehydrated, and air-dried for cultivating in hybridization buffer with LINC01116-specific RNA fluorescence in situ hybridization (FISH) probe (Ribobio).

Techniques: Software, Quantitative RT-PCR, Expressing, Transfection, Pull Down Assay, Western Blot

Journal: Cell Death & Disease

Article Title: LINC01106 post-transcriptionally regulates ELK3 and HOXD8 to promote bladder cancer progression

doi: 10.1038/s41419-020-03236-9

Figure Lengend Snippet: Four groups of J82 and T24 cells were involved, including sh-NC, sh-LINC01116#1, sh-LINC01116#1 + pcDNA3.1/ELK3, sh-LINC01116#1 + pcDNA3.1/ELK3 + pcDNA3.1/HOXD8. a , b Colony formation assay and EdU assay detected the proliferation ability of cells in these four groups. c Flow cytometry analysis detected the apoptosis rate of cells in these four groups. d , e Transwell assays detected the migration and invasion capacity of indicated J28 and T24 cells. f Western blot examined the expression of E-cadherin, N-cadherin, and Vimentin in indicated J28 and T24 cells. * P < 0.05, ** P < 0.01.

Article Snippet: The fixed J82 and T24 cells were rinsed in PBS, dehydrated, and air-dried for cultivating in hybridization buffer with LINC01116-specific RNA fluorescence in situ hybridization (FISH) probe (Ribobio).

Techniques: Colony Assay, EdU Assay, Flow Cytometry, Migration, Western Blot, Expressing

Journal: Cell Death & Disease

Article Title: LINC01106 post-transcriptionally regulates ELK3 and HOXD8 to promote bladder cancer progression

doi: 10.1038/s41419-020-03236-9

Figure Lengend Snippet: a The expression of LINC01116 was examined in J82 and T24 cells transfected with shRNAs targeting HOXD8 or ELK3 by RT-qPCR. b ChIP assay was further conducted to explore the functional relationship between LINC01116 and HOXD8. c Five binding sites between LINC01116 promoter and HOXD8 were predicted using JASPAR software. d Luciferase reporter gene assays were performed to verify which site in LINC01116 promoter was recognized by HOXD8. e Luciferase reporter assays also detected the influence of HOXD8 on the activity of P1. * P < 0.05, ** P < 0.01.

Article Snippet: The fixed J82 and T24 cells were rinsed in PBS, dehydrated, and air-dried for cultivating in hybridization buffer with LINC01116-specific RNA fluorescence in situ hybridization (FISH) probe (Ribobio).

Techniques: Expressing, Transfection, Quantitative RT-PCR, Functional Assay, Binding Assay, Software, Luciferase, Activity Assay

Journal: Cell Death & Disease

Article Title: LINC01106 post-transcriptionally regulates ELK3 and HOXD8 to promote bladder cancer progression

doi: 10.1038/s41419-020-03236-9

Figure Lengend Snippet: The drawing analyzed the two functional pathways of LINC01116-miR-3612-ELK3 and LINC01116-DKC1-HOXD8 in BCa cells. * P < 0.05, ** P < 0.01.

Article Snippet: The fixed J82 and T24 cells were rinsed in PBS, dehydrated, and air-dried for cultivating in hybridization buffer with LINC01116-specific RNA fluorescence in situ hybridization (FISH) probe (Ribobio).

Techniques: Functional Assay