Journal: Frontiers in Fungal Biology

Article Title: Genome-Wide Association for Itraconazole Sensitivity in Non-resistant Clinical Isolates of Aspergillus fumigatus

doi: 10.3389/ffunb.2020.617338

Figure Lengend Snippet: Characterization of SNPs associated with ITCZ sensitivity.

Article Snippet: 2 , 541570 , T , C , 0.00109 , 0.00231196 , Afu2g02170 , 5 prime UTR variant.

Techniques: Variant Assay

Journal: Animals : an Open Access Journal from MDPI

Article Title: Genomic Characterization of the Istrian Shorthaired Hound

doi: 10.3390/ani10112013

Figure Lengend Snippet: Genomic regions with the highest iHS values.

Article Snippet: BICF2G630167445 , 4 , 36002909 , 4.374 , 4.915 , Upstream gene variant of the gene RGS14 (3,6 kbp), 5 prime UTR variant of LMAN2 , downstream variant of the gene F12 (4.9 kbp)..

Techniques: Variant Assay

Journal:

Article Title: Integration of HIV-1 caused STAT3-associated B cell lymphoma in an AIDS patient

doi: 10.1016/j.micinf.2007.09.008

Figure Lengend Snippet: (A) Sequence of the HIV-1 5’-LTR (upper panel) and 3’-LTR (lower panel) insertion site in the lymphoma genome. Whole sequences of PCR products are registered as GenBank DQ355432 (5’-LTR, 190 bp) and DQ117603 (3’-LTR, 1.5 kbp), respectively. The sequence of the lymphoma genome is shown in the lower line in black letters. The upper colored line indicates the HIV-1 LTR sequence (blue, GenBank K03455 or AF538307) and STAT3 genomic sequence (violet, GenBank AY572796). HIV-1 intervening sequence between 5’LTR and gag is indicated by green. Duplication of the cellular 5 bp (GAATC) and additional dinucleotides (TG in 5’-LTR and CA in 3’-LTR) by HIV-1 integrase are underlined. DraI site is indicated by italics. (B) PCR for the junction region of 3’LTR and STAT3 gene using HIV3LTR-F and Stat3intron-R primers (see Fig. 3D). 1, PBMCs from a healthy donor; 2, HIV-1-positive Molt4 cell line; 3, lymphoma cells with HIV-1integration; 4, KS lesion from the patient; 5, AIDS-related lymphoma from an unrelated patient; 6, lymphoma from a non-HIV-1infected patient; 7, BCBL-1 (KSHV-positive B cell line); 8, No DNA. The lower panel shows the results of an internal control (β-globin gene). (C) PCR of genomic DNA with a STAT3-intron forward primer (F in this figure, Stat3-intronF2) in combination with 5’ LTR reverse primers (lanes 1–6, 55R, 78R, 348R, 495R, 563R and 612R), and a reverse primer positioning between 5’LTR and gag (lane 7, 676R). The upper panel shows the positions of these primers. A 188 bp product was identified when the 676R primer was used with the STAT3 intron primer (lane 7). If the 5’LTR was intact, the predicted size of this amplicon would have been 777 bp. (D) Map of the defective HIV-1 insertion site in the STAT3 gene. Violet numbers indicate the number in GenBank AY572796 (STAT3). Blue boxes are HIV-1 genomes.

Article Snippet: The cells were transfected with STAT3 expression vector by Nucleofector (Amaxa, Cologne, Germany) using O-06 program.

Techniques: Sequencing, Amplification

Journal:

Article Title: Integration of HIV-1 caused STAT3-associated B cell lymphoma in an AIDS patient

doi: 10.1016/j.micinf.2007.09.008

Figure Lengend Snippet: (A) Probe-primer sets for real time PCR. The top line with boxes is a genome map around HIV-1 integration site of HIV-1 3’LTR. Numbers with plus and minus under the genome map indicate distances (bp) from the integration site. Arrows and heavy lines are probe-primer sets of real time PCR. (B) Copy numbers of HIV-1 integration site and STAT3 gene. Black, gray and white bars indicate mean copy number per 100 ng DNA of this case, HIV-1-positive Molt4 cell line, and TY-1 (HIV-1-negative, KSHV-positive B cell line), respectively. Copy numbers per 100 ng DNA are indicated on the top of each bar. Error bars indicate standard errors of triplicate samples.

Article Snippet: The cells were transfected with STAT3 expression vector by Nucleofector (Amaxa, Cologne, Germany) using O-06 program.

Techniques: Real-time Polymerase Chain Reaction

Journal:

Article Title: Integration of HIV-1 caused STAT3-associated B cell lymphoma in an AIDS patient

doi: 10.1016/j.micinf.2007.09.008

Figure Lengend Snippet: (A) Promoter activity of HIV-1 3’LTR by reporter assay. Schematic representation of promoter constructs used in transient transfection assays is shown on the left. Forty-eight hours after transfection, cells were collected and the luciferase activity was measured. The percentage relative luminescence units (RLU) were calculated by dividing firefly activity by renilla activity. Horizontal bars indicate standard deviations of three independent experiments. (B and C) No methylation in a promoter enhancer region of HIV-1 3’LTR in the HIV-1-integrated lymphoma. (B) CpG sites in the promoter enhancer region of 3’LTR of the HIV-1 provirus in the patient with HIV-1-integrated lymphoma (218-529 in GenBank DQ117603). CpG sites are in boldface and numbered from the 5’ end of the LTR (1–11). Nuclear factor-κB and Sp1 sites identified with Motif Search (Kyoto University Bioinfomatics center, Kyoto, Japan, http://motif.genome.jp/) at a 75% cut-off value are indicated by boxes with broken and solid lines, respectively. Sequences used for primers are indicated by underlining. (C) Levels of CpG methylation of the promoter enhancer region of HIV-1 3’LTR in the HIV-1-integrated lymphoma and lymph nodes in the patient. Results of bisulfite genomic sequencing coupled with TA cloning are shown. The methylation status of 10 clones for each sample is presented; methylation of each CpG site is expressed as a filled circle, and unmethylated sites are shown as open circles. Top, schematic description of CpG sites in the 3’LTR of (B). (D-F) Immunohistochemistry of STAT3. The HIV-1-integrated lymphoma cells expressed STAT3 predominantly in the nucleus (D), however, signals of STAT3 were weak and localized in the cytoplasm in the other case of KSHV-positive, AIDS-related lymphoma (E), and were very weak in a case of EBV-positive, AIDS-related lymphoma (F). Original magnification is x400.

Article Snippet: The cells were transfected with STAT3 expression vector by Nucleofector (Amaxa, Cologne, Germany) using O-06 program.

Techniques: Activity Assay, Reporter Assay, Construct, Transfection, Luciferase, Methylation, CpG Methylation Assay, Genomic Sequencing, TA Cloning, Clone Assay, Immunohistochemistry

Journal:

Article Title: Integration of HIV-1 caused STAT3-associated B cell lymphoma in an AIDS patient

doi: 10.1016/j.micinf.2007.09.008

Figure Lengend Snippet: STAT3 expression in AIDS-related and unrelated lymphoma.

Article Snippet: The cells were transfected with STAT3 expression vector by Nucleofector (Amaxa, Cologne, Germany) using O-06 program.

Techniques: Expressing

Journal:

Article Title: Integration of HIV-1 caused STAT3-associated B cell lymphoma in an AIDS patient

doi: 10.1016/j.micinf.2007.09.008

Figure Lengend Snippet: (A) STAT3 expression in the STAT3-transfected TY-1, a KSHV-positive B cell line. The cells were transfected with STAT3 expression vector by Nucleofector (Amaxa, Cologne, Germany) using O-06 program. STAT3 expression was detected by anti-STAT3 mouse monoclonal antibody (green in left panel) and anti-6xHis antibody, followed by Alexa 488-conjugated anti-mouse IgG antibody (Molecular probe, green in right panel). Red color indicates nuclear counterstaining of propidium iodide. (B) Localization of transfected STAT3 in TY-1. His-tagged STAT3 was detected by anti-6x His antibody in the cytoplasm of B cells (left panel). In the presence of IL-6 (Peprotech, Rocky Hill, NJ, 0.1 ng/ml), transfected STAT3 localizes in the nucleus predominantly (right panel). (C) Cell proliferation assay for STAT3-transfected primary B lymphocytes. Primary B cells were isolated from PBMC. The purity of B cell (CD19+) was >95%. The cells were transfected with STAT3 expression vector expressing STAT3 and CD4 by Nucleofector using U-15 program. Transfection efficiency to primary B cells was around 20%. To increase the proportion of transfected cells, the transfected B cells were separated with CD4 microbeads after 16 hours of the transfection (Miltenyl Biotec, Auburn CA). 48 hours after transfection of STAT3 or vector to primary B cells, the proliferation rate was measured with BrdU ELISA (Roche). Raji is an EBV-positive Burkitt lymphoma cell line (untransfected). Numbers in Y-axis indicates absorbance in ELISA. Error bars indicate standard errors of 8 independent experiments.

Article Snippet: The cells were transfected with STAT3 expression vector by Nucleofector (Amaxa, Cologne, Germany) using O-06 program.

Techniques: Expressing, Transfection, Plasmid Preparation, Proliferation Assay, Isolation, Enzyme-linked Immunosorbent Assay

Journal: Pharmacogenomics and Personalized Medicine

Article Title: Analysis of Very Important Pharmacogenomics Variants in the Chinese Lahu Population

doi: 10.2147/PGPM.S324410

Figure Lengend Snippet: Basic Characteristics Selected Variants in the Lahu

Article Snippet: 3 , NR1I2 , 119781188 , rs3814055 , Upstream variant 2KB, utr variant 5 prime , T/C , 0.22 , 0.79.

Techniques: Functional Assay, Variant Assay

Journal: Genes

Article Title: Association between SNPs in Leptin Pathway Genes and Anthropometric, Biochemical, and Dietary Markers Related to Obesity

doi: 10.3390/genes13060945

Figure Lengend Snippet: List of 74 genetic variants evaluated in the study.

Article Snippet: rs34114122 , T > G , 5 prime UTR variant.

Techniques: Variant Assay, Functional Assay, Sequencing

Journal: Genes

Article Title: Association between SNPs in Leptin Pathway Genes and Anthropometric, Biochemical, and Dietary Markers Related to Obesity

doi: 10.3390/genes13060945

Figure Lengend Snippet: Genetic frequencies of evaluated variants.

Article Snippet: rs34114122 , T > G , 5 prime UTR variant.

Techniques:

Journal: Genes

Article Title: Association between SNPs in Leptin Pathway Genes and Anthropometric, Biochemical, and Dietary Markers Related to Obesity

doi: 10.3390/genes13060945

Figure Lengend Snippet: Significant statistical associations between clinical markers of obesity and SNPs of LEP, LEPR, POMC, PCSK1, and MC4R, considered to be risk factors.

Article Snippet: rs34114122 , T > G , 5 prime UTR variant.

Techniques: Marker, Fat

Journal: Scientific Reports

Article Title: Kernel machine SNP set analysis finds the association of BUD13, ZPR1, and APOA5 variants with metabolic syndrome in Tehran Cardio-metabolic Genetics Study

doi: 10.1038/s41598-021-89509-5

Figure Lengend Snippet: Characteristics of the Markers in selected chromosomal region.

Article Snippet: APOA5 , 5 prime UTR variant , rs651821 , 11:116791863 , T:C , 0.14 , 0.18 , C , 0.14.

Techniques: Variant Assay