Journal: BMC Infectious Diseases

Article Title: Vaginal microbiome in women from Greenland assessed by microscopy and quantitative PCR

doi: 10.1186/1471-2334-13-480

Figure Lengend Snippet: Sensitivity and specificity before (qualitative detection 1 ) and after (quantitative detection 2 ) applying ROC curve analysis

Article Snippet: Positive controls and specificity controls for the PCRs were obtained by DNA extraction from culture collection strains of Atopobium vaginae (CCUG 38953 T ), Sneathia sanguinegenes (CCUG 41628 T ), Leptotrichia amnionii (DSM 16630), Mobiluncus curtisii (CCUG 21018 T ), M. mulieris (CCUG 20071 T ), Lactobacillus iners (CCUG 28746 T ), L. crispatus (CCUG 30722), L. gasseri (DSM 14869), L. jensenii (CCUG 21961), Gardnerella vaginalis (ATCC 3717 T ), Mycoplasma hominis (ATCC 15488) , Ureaplasma parvum (ATCC 27815 T ) , U. urealyticum (ATCC 27618 T ), Finegoldia magna (DSM 20470 T ), Peptostreptococcus anaerobius (CCUG 7835), and Veillonella montpellierensis (CCUG 48299), and from clinical isolates of Prevotella oris , P. bivia (2 different strains), P. nigrescens (2 different strains), P. buccae (2 different strains), P. loeschii, and P. intermedia identified by biochemical properties and MALDI-TOF and/or sequencing of 16S rRNA genes.

Techniques:

Journal: BMC Infectious Diseases

Article Title: Vaginal microbiome in women from Greenland assessed by microscopy and quantitative PCR

doi: 10.1186/1471-2334-13-480

Figure Lengend Snippet: Proportion of women in which non- Lactobacillus species were detected

Article Snippet: Positive controls and specificity controls for the PCRs were obtained by DNA extraction from culture collection strains of Atopobium vaginae (CCUG 38953 T ), Sneathia sanguinegenes (CCUG 41628 T ), Leptotrichia amnionii (DSM 16630), Mobiluncus curtisii (CCUG 21018 T ), M. mulieris (CCUG 20071 T ), Lactobacillus iners (CCUG 28746 T ), L. crispatus (CCUG 30722), L. gasseri (DSM 14869), L. jensenii (CCUG 21961), Gardnerella vaginalis (ATCC 3717 T ), Mycoplasma hominis (ATCC 15488) , Ureaplasma parvum (ATCC 27815 T ) , U. urealyticum (ATCC 27618 T ), Finegoldia magna (DSM 20470 T ), Peptostreptococcus anaerobius (CCUG 7835), and Veillonella montpellierensis (CCUG 48299), and from clinical isolates of Prevotella oris , P. bivia (2 different strains), P. nigrescens (2 different strains), P. buccae (2 different strains), P. loeschii, and P. intermedia identified by biochemical properties and MALDI-TOF and/or sequencing of 16S rRNA genes.

Techniques:

Journal: BMC Infectious Diseases

Article Title: Vaginal microbiome in women from Greenland assessed by microscopy and quantitative PCR

doi: 10.1186/1471-2334-13-480

Figure Lengend Snippet: Odds-ratios (OR) and 95% confidence intervals (CI) (Fisher’s exact test) for BV

Article Snippet: Positive controls and specificity controls for the PCRs were obtained by DNA extraction from culture collection strains of Atopobium vaginae (CCUG 38953 T ), Sneathia sanguinegenes (CCUG 41628 T ), Leptotrichia amnionii (DSM 16630), Mobiluncus curtisii (CCUG 21018 T ), M. mulieris (CCUG 20071 T ), Lactobacillus iners (CCUG 28746 T ), L. crispatus (CCUG 30722), L. gasseri (DSM 14869), L. jensenii (CCUG 21961), Gardnerella vaginalis (ATCC 3717 T ), Mycoplasma hominis (ATCC 15488) , Ureaplasma parvum (ATCC 27815 T ) , U. urealyticum (ATCC 27618 T ), Finegoldia magna (DSM 20470 T ), Peptostreptococcus anaerobius (CCUG 7835), and Veillonella montpellierensis (CCUG 48299), and from clinical isolates of Prevotella oris , P. bivia (2 different strains), P. nigrescens (2 different strains), P. buccae (2 different strains), P. loeschii, and P. intermedia identified by biochemical properties and MALDI-TOF and/or sequencing of 16S rRNA genes.

Techniques:

Journal: Cureus

Article Title: The prevalence of Mycoplasma hominis in Outpatients at a Tertiary Care Hospital in East India

doi: 10.7759/cureus.31110

Figure Lengend Snippet: Ethidium bromide strained 2% agar gel shows the PCR amplification product with 16SrRNA gene for Mycoplasma hominis. Lanes 6 and 14 are positive for Mycoplasma hominis with 687 base pair product.

Article Snippet: The PCR-positive control was DNA extracted from M. hominis ATCC 15488.

Techniques: Amplification

Journal: Neuropathology

Article Title: Praja1 RING ‐finger E3 ubiquitin ligase suppresses neuronal cytoplasmic TDP ‐43 aggregate formation

doi: 10.1111/neup.12694

Figure Lengend Snippet: PCR primers used in this study

Article Snippet: The blotted membrane was blocked with 3% skim milk and incubated overnight with rabbit anti‐FLAG (#7425; Sigma), rabbit anti‐TDP‐43 C‐terminus (405‐414) (#TIP‐TDP09; Cosmo Bio, Tokyo, Japan), rabbit anti‐phosphorylated TDP‐43 (pSer409/S410) (#TIP‐PTD‐P02; Cosmo Bio), rabbit anti‐PJA1 (#17687‐1‐AP; ProteinTech Japan, Tokyo, Japan), rabbit anti‐Myc Tag (#2278; Cell Signaling Technology, Danvers, MA, USA), rabbit anti‐ubiquitin K48 (#05‐1307; Sigma), rabbit anti‐UBE2D2/3 (#HPA003921: Sigma), rabbit anti‐UBE2E3 (#15488‐1‐AP; ProteinTech), rabbit anti‐UBE2K (#11834‐3‐AP; ProteinTech), and mouse monoclonal anti‐GAPDH (#ab8245; Abcam, Cambridge, UK) antibodies at dilutions of 1:1000, followed by incubation with biotinylated anti‐rabbit or anti‐mouse IgG (Vector Laboratories, Burlingame, CA, USA; 1:1000) for 1 h and streptavidin‐alkaline phosphatase (#11089161001; Sigma; 1:1000) for 1 h. Reactions were visualized by color development using nitroblue tetrazolium chloride (NBT) and 5‐bromo‐4‐chloro‐3‐indolylphosphate p‐toluidine salt (BCIP) (#11681451001; Sigma).

Techniques:

Journal: Neuropathology

Article Title: Praja1 RING ‐finger E3 ubiquitin ligase suppresses neuronal cytoplasmic TDP ‐43 aggregate formation

doi: 10.1111/neup.12694

Figure Lengend Snippet: PJA1 binding to TDP‐43 and E2 ubiquitin conjugating enzyme UBE2E3. (A) Western blot analysis of suppressive effects of adenovirus expressing human PJA1v1, but not PJA1ΔR, on phosphorylation and aggregate formation of TDP‐43 after DsRed‐ and FLAG‐tagged wild‐type (WT) and CTF TDP‐43 adenovirus infection in the presence of 0.5 μM MG‐132 (lanes 3–8). The CTF TDP‐43 adenovirus preferably induces RIPA‐insoluble phosphorylated TDP‐43 (lanes 4, 6). Adenovirally‐induced hPJA1v1 and hPJA1ΔR is consistently localized in both RIPA‐soluble and insoluble fractions (lanes 3, 5, 7, 8), and adenoviral hPJA1v1, but not hPJA1ΔR, decreases RIPA‐insoluble phosphorylated CTF TDP‐43 (lanes 5, 7) in a similar manner to the experiment shown in Figure . Endogenous UBE2E3 is also detected both in RIPA‐soluble and insoluble fractions. (B) The co‐immunoprecipitation (Co‐IP) assay shows that PJA1 preferentially binds to CTF TDP‐43 rather than WT TDP‐43 (PJA1 blot; lanes 3, 5, 7, 8), while CTF TDP‐43 is consistently ubiquitinated irrespective of adenoviral PJA1 induction (Ubiquitin K48 blot; lanes 4–8). Both native and adenoviral UBE2E3 are co‐immunoprecipitated with WT and CTF TDP‐43 (UBE2E3 and Myc‐Tag blots). (C) Co‐IP assay indicates that TDP‐43 and/or PJA1 bind to UBE2E3 but not UBE2D2/3 or UBE2K. (D) Fluorescence micrographs of TuJ1‐immunoreactive differentiated neurons co‐infected with DsRed‐tagged WT and CTF TDP‐43 adenoviruses and EGFP‐tagged hPJA1v1 (top row) or hPJA1ΔR (bottom row) adenovirus in the presence of 0.5 μM MG‐132. The nucleus is counterstained with Hoechst 33342. Two types of co‐localization (i.e., perinuclear round fluorescence [arrows] and cytoplasmic amorphous aggregates [arrowheads]), are observed.

Article Snippet: The blotted membrane was blocked with 3% skim milk and incubated overnight with rabbit anti‐FLAG (#7425; Sigma), rabbit anti‐TDP‐43 C‐terminus (405‐414) (#TIP‐TDP09; Cosmo Bio, Tokyo, Japan), rabbit anti‐phosphorylated TDP‐43 (pSer409/S410) (#TIP‐PTD‐P02; Cosmo Bio), rabbit anti‐PJA1 (#17687‐1‐AP; ProteinTech Japan, Tokyo, Japan), rabbit anti‐Myc Tag (#2278; Cell Signaling Technology, Danvers, MA, USA), rabbit anti‐ubiquitin K48 (#05‐1307; Sigma), rabbit anti‐UBE2D2/3 (#HPA003921: Sigma), rabbit anti‐UBE2E3 (#15488‐1‐AP; ProteinTech), rabbit anti‐UBE2K (#11834‐3‐AP; ProteinTech), and mouse monoclonal anti‐GAPDH (#ab8245; Abcam, Cambridge, UK) antibodies at dilutions of 1:1000, followed by incubation with biotinylated anti‐rabbit or anti‐mouse IgG (Vector Laboratories, Burlingame, CA, USA; 1:1000) for 1 h and streptavidin‐alkaline phosphatase (#11089161001; Sigma; 1:1000) for 1 h. Reactions were visualized by color development using nitroblue tetrazolium chloride (NBT) and 5‐bromo‐4‐chloro‐3‐indolylphosphate p‐toluidine salt (BCIP) (#11681451001; Sigma).

Techniques: Binding Assay, Western Blot, Expressing, Infection, Co-Immunoprecipitation Assay, Immunoprecipitation, Fluorescence