Journal: BMC Bioinformatics

Article Title: Nonparametric methods for the analysis of single-color pathogen microarrays

doi: 10.1186/1471-2105-11-354

Figure Lengend Snippet: Viral isolates

Article Snippet: The data pool included three single-stranded positive sense RNA viruses: West Nile virus (WNV, strain New York 1999, AF202541, ca 11 kb), SARS coronavirus (HCoV-SARS, strain Tor2, AY274119, ca 30 kb), and human echovirus 18 (EV18, strain Metcalf, ATCC VR-48, AF317694, ca 7.4 kb); two segmented single-stranded negative sense RNA viruses: Lassa virus (LASV, strain Josiah, ca 3.4 kb and 7.3 kb) and influenza A virus H1N1 (FLUA H1N1; A/Texas/36/91, CY009316-CY009323, 8 segments of ca 2.3, 2.3, 2.2, 1.7, 1.5, 1.4,1 and 0.9 kb); two non-segmented single-stranded negative sense RNA viruses: Zaire ebolavirus (ZEBOV, NC_002549, ca 19 kb) and vesicular stomatitis virus (VSV, Indiana strain, NC_001560, ca 11.1 kb); and two double-stranded DNA viruses: human adenovirus 4 (HAdV-4, ATCC VR-1572, NC_003266, ca 36 kb) and human herpesvirus 1 (HSV-1, viral culture, NC_001806, ca 152 kb) (see Table ; data available in GEO Series GSE21318 and Additional File ).

Techniques: Virus

Journal: BMC Bioinformatics

Article Title: Nonparametric methods for the analysis of single-color pathogen microarrays

doi: 10.1186/1471-2105-11-354

Figure Lengend Snippet: False positive rates for methods of pathogen identification

Article Snippet: The data pool included three single-stranded positive sense RNA viruses: West Nile virus (WNV, strain New York 1999, AF202541, ca 11 kb), SARS coronavirus (HCoV-SARS, strain Tor2, AY274119, ca 30 kb), and human echovirus 18 (EV18, strain Metcalf, ATCC VR-48, AF317694, ca 7.4 kb); two segmented single-stranded negative sense RNA viruses: Lassa virus (LASV, strain Josiah, ca 3.4 kb and 7.3 kb) and influenza A virus H1N1 (FLUA H1N1; A/Texas/36/91, CY009316-CY009323, 8 segments of ca 2.3, 2.3, 2.2, 1.7, 1.5, 1.4,1 and 0.9 kb); two non-segmented single-stranded negative sense RNA viruses: Zaire ebolavirus (ZEBOV, NC_002549, ca 19 kb) and vesicular stomatitis virus (VSV, Indiana strain, NC_001560, ca 11.1 kb); and two double-stranded DNA viruses: human adenovirus 4 (HAdV-4, ATCC VR-1572, NC_003266, ca 36 kb) and human herpesvirus 1 (HSV-1, viral culture, NC_001806, ca 152 kb) (see Table ; data available in GEO Series GSE21318 and Additional File ).

Techniques: Negative Control

Journal: BMC Bioinformatics

Article Title: Nonparametric methods for the analysis of single-color pathogen microarrays

doi: 10.1186/1471-2105-11-354

Figure Lengend Snippet: Positive predictive value for methods of pathogen identification

Article Snippet: The data pool included three single-stranded positive sense RNA viruses: West Nile virus (WNV, strain New York 1999, AF202541, ca 11 kb), SARS coronavirus (HCoV-SARS, strain Tor2, AY274119, ca 30 kb), and human echovirus 18 (EV18, strain Metcalf, ATCC VR-48, AF317694, ca 7.4 kb); two segmented single-stranded negative sense RNA viruses: Lassa virus (LASV, strain Josiah, ca 3.4 kb and 7.3 kb) and influenza A virus H1N1 (FLUA H1N1; A/Texas/36/91, CY009316-CY009323, 8 segments of ca 2.3, 2.3, 2.2, 1.7, 1.5, 1.4,1 and 0.9 kb); two non-segmented single-stranded negative sense RNA viruses: Zaire ebolavirus (ZEBOV, NC_002549, ca 19 kb) and vesicular stomatitis virus (VSV, Indiana strain, NC_001560, ca 11.1 kb); and two double-stranded DNA viruses: human adenovirus 4 (HAdV-4, ATCC VR-1572, NC_003266, ca 36 kb) and human herpesvirus 1 (HSV-1, viral culture, NC_001806, ca 152 kb) (see Table ; data available in GEO Series GSE21318 and Additional File ).

Techniques:

Journal: Oncotarget

Article Title: IGF-I induces upregulation of DDR1 collagen receptor in breast cancer cells by suppressing MIR-199a-5p through the PI3K/AKT pathway

doi: 10.18632/oncotarget.6524

Figure Lengend Snippet: ( A–B ) Constitutively active AKT and ERK1/2 and DDR1 upregulation in IGF-II transfected cells. (A) MCF-7 and (B) MDA-MB-231 cells were transfected with a c-Myc tagged IGF-II expression construct (IGF-II) or a control empty vector (EV). Cells were solubilized and samples analyzed by western blotting with anti-DDR1, phospho-IGF-IR, phospho-S473-AKT and phospho-ERK1/2 antibodies. The same blots were probed with anti-AKT, anti-ERK1/2, anti-β-actin, and anti-c-Myc antibodies to check for protein loading and cell transfection efficiency. Both cell lines showed constitutively active IGF-IR, AKT and ERK1/2 and significant increase in DDR1 protein and DDR1 mRNA ( C–D ) in IGF-II transfected cells. Each blot is representative of three independent experiments. Values shown in graphs are mean ± SEM of three independent experiments. * P < 0.05. ( E–F ) Inhibition of miR-199a-5p in IGF-II transfected cells. In cell transfected as above, miR-199a-5p expression levels significantly decreased. Values shown in graphs are mean ± SEM of three independent experiments. * P < 0.05; *** P < 0.0001.

Article Snippet: Construct encoding 3′UTR clone of DDR1 in pMirTarget Vector, the related empty vector (pCMV6) and the human IGF-II cDNAs were from OriGene Technologies (Rockville, USA).

Techniques: Transfection, Expressing, Construct, Plasmid Preparation, Western Blot, Inhibition

Journal: Oncotarget

Article Title: IGF-I induces upregulation of DDR1 collagen receptor in breast cancer cells by suppressing MIR-199a-5p through the PI3K/AKT pathway

doi: 10.18632/oncotarget.6524

Figure Lengend Snippet: MCF-7 and MDA-MB-231 cells, stably transfected with either pcDNA3.1HA-myr-AKT, control pcDNA3.1HA ( A – B ), or with c-Myc tagged IGF-II expression construct or the relative empty vector ( C–D ), were starved for 24 h and then transfected with 100 nM miR199a-5p or scramble oligonucleotides for 48 h. Cells were then evaluated by western blotting for DDR1 expression with a polyclonal antibody against the C-terminus of DDR1. In myr-AKT transfected cells AKT expression was also evaluated. β-actin was used as control for protein loading.

Article Snippet: Construct encoding 3′UTR clone of DDR1 in pMirTarget Vector, the related empty vector (pCMV6) and the human IGF-II cDNAs were from OriGene Technologies (Rockville, USA).

Techniques: Stable Transfection, Transfection, Expressing, Construct, Plasmid Preparation, Western Blot