Journal: Proceedings of the National Academy of Sciences of the United States of America

Article Title: CNS expression of glucocerebrosidase corrects ?-synuclein pathology and memory in a mouse model of Gaucher-related synucleinopathy

doi: 10.1073/pnas.1108197108

Figure Lengend Snippet: Ubiquitin and α-syn aggregates colocalize with neuronal markers. Sections of hippocampus in 12-mo-old Gba1 D409V/D409V brains, either pretreated with proteinase K (PK) ( B ) or not ( A and C ) before immunostaining. Immunostaining for NFH ( A ) exposed

Article Snippet: Some tissue sections were pretreated with proteinase K (1:4 dilution; DAKO) for 7 min at room temperature to expose α-syn and other aggregated proteins ( ).

Techniques: Immunostaining

Journal: Proceedings of the National Academy of Sciences of the United States of America

Article Title: CNS expression of glucocerebrosidase corrects ?-synuclein pathology and memory in a mouse model of Gaucher-related synucleinopathy

doi: 10.1073/pnas.1108197108

Figure Lengend Snippet: Progressive accumulation of α-syn/ubiquitin aggregates in Gba1 D409V/D409V Gaucher mouse brains. ( A ) Frozen sections were pretreated without ( Upper ) or with ( Lower ) proteinase K (PK) to uncover endogenous α-syn aggregates (arrowheads).

Article Snippet: Some tissue sections were pretreated with proteinase K (1:4 dilution; DAKO) for 7 min at room temperature to expose α-syn and other aggregated proteins ( ).

Techniques:

Journal: Molecular and Cellular Biology

Article Title: A Protease-Resistant 61-Residue Prion Peptide Causes Neurodegeneration in Transgenic Mice

doi: 10.1128/MCB.21.7.2608-2616.2001

Figure Lengend Snippet: Treatment of ScN2a cells with PPI. ScN2a cells were transfected transiently with the pSPOX expression vector encoding either the full-length MHM2 or the MHM2(Δ23–88,Δ141–221) sequence. Three days after transfection cells were incubated with either control medium or medium plus 150 μg of PPI generation 4.0 per ml for 4 h. Cells were then harvested and lysed as described in Materials and Methods. Minus symbols denote undigested control lysate, and plus symbols designate the pellet fraction of lysate subjected to limited proteolysis with 20 μg of proteinase K per ml for 1 h at 37°C, corresponding to a total protein/proteinase K ratio of 25:1. Units are apparent molecular sizes based on migration of protein standards in kilodaltons. Lane 1, MHM2 control; lane 2, MHM2 plus PPI; lane 3, PrP61 control; lane 4, PrP61 plus PPI.

Article Snippet: Proteinase K (Boehringer Mannheim) was added to 0.5 ml of adjusted homogenate to achieve a ratio of total protein to enzyme of 50:1.

Techniques: Transfection, Expressing, Plasmid Preparation, Sequencing, Incubation, Migration

Journal: Molecular and Cellular Biology

Article Title: A Protease-Resistant 61-Residue Prion Peptide Causes Neurodegeneration in Transgenic Mice

doi: 10.1128/MCB.21.7.2608-2616.2001

Figure Lengend Snippet: Expression of PrP deletion constructs in scrapie-infected neuroblastoma cells. Scrapie-infected (ScN2a) cells were transfected transiently with the pSPOX expression vector carrying modified PrP genes as noted below. Lane 1, MHM2; lane 2, MHM2(Δ23–88); lane 3, MHM2(Δ23–88,Δ141–176); lane 4, MHM2(Δ23–88,Δ127–176); lane 5, MHM2(Δ23–88,Δ127–164); lane 6, mock transfection. Minus symbols denote undigested control sample, and plus symbols designate the pellet fraction of sample subjected to limited proteolysis with 7 μg of proteinase K per ml for 30 min at 37°C, corresponding to a total protein/proteinase K ratio of 71:1. Units are apparent molecular sizes based on migration of protein standards in kilodaltons.

Article Snippet: Proteinase K (Boehringer Mannheim) was added to 0.5 ml of adjusted homogenate to achieve a ratio of total protein to enzyme of 50:1.

Techniques: Expressing, Construct, Infection, Transfection, Plasmid Preparation, Modification, Migration

Journal: Molecular and Cellular Biology

Article Title: A Protease-Resistant 61-Residue Prion Peptide Causes Neurodegeneration in Transgenic Mice

doi: 10.1128/MCB.21.7.2608-2616.2001

Figure Lengend Snippet: ). None, no fragments detected with MAb 3F4 after digestion with 7 μg of proteinase K per ml for 30 min at 37°C; ++, fragments detected after digestion with 7 μg of proteinase K per ml for 30 min at 37°C but not after digestion with 20 μg of proteinase K per ml for 1 h at 37°C; ++++, intense 3F4 immunoreactive fragments seen even after digestion with 20 μg of proteinase K per ml for 1 h at 37°C. HA, α-helix A; HB, α-helix B; HC, α-helix C; CHO, carbohydrate; S-S, disulfide bond.

Article Snippet: Proteinase K (Boehringer Mannheim) was added to 0.5 ml of adjusted homogenate to achieve a ratio of total protein to enzyme of 50:1.

Techniques:

Journal: Molecular and Cellular Biology

Article Title: A Protease-Resistant 61-Residue Prion Peptide Causes Neurodegeneration in Transgenic Mice

doi: 10.1128/MCB.21.7.2608-2616.2001

Figure Lengend Snippet: Protease digestion of MHM2(Δ23–88,Δ141–221). (A) Lanes A1 through A3, N2a cells transfected with pSPOX[MHM2(Δ23–88,Δ141–221)]; lanes B1 through B3, mock-transfected N2a cells; lanes C1 through C3, 0.4 μg of myristylated, synthetic MHM2(Δ23–88,Δ141–221) peptide per ml mixed with untransfected N2a cell lysate (0.5 mg of total protein per ml). Lanes A1, B1, and C1, untreated whole-cell lysates; lanes A2, B2, and C2, pellet fractions of lysates digested with 7 μg of proteinase K per ml for 30 min at 37°C; lanes A3, B3, and C3, pellet fractions of lysates digested with 20 μg of proteinase K per ml for 1 h at 37°C. SDS-PAGE was performed on 16% Tricine gels (Novex). Western blotting was performed with 3F4 MAb at 1:5,000 dilution. After processing, lanes 1 and 2 were exposed for 1 min and lane 3 was exposed for 15 min to Hypermax film (Amersham Life Sciences). Units are apparent molecular sizes based on migration of protein standards in kilodaltons. (B) Proteinase K digestion of brain homogenates from Tg mice. Lane 1, 60-day-old, uninoculated Tg(PrP106)Prnp 0/0 mouse; lane 2, 65-day-old, scrapie-infected Tg(PrP106)Prnp 0/0 mouse; lane 3, 48-day-old, spontaneously ataxic Tg(PrP61)Prnp 0/0 mouse. Minus symbols denote undigested control sample, and plus symbols designate the pellet fraction of sample subjected to digestion with 20 μg of proteinase K per ml for 1 h at 37°C. Units are apparent molecular sizes based on migration of protein standards in kilodaltons.

Article Snippet: Proteinase K (Boehringer Mannheim) was added to 0.5 ml of adjusted homogenate to achieve a ratio of total protein to enzyme of 50:1.

Techniques: Transfection, SDS Page, Western Blot, Migration, Mouse Assay, Infection

Journal: PLoS Pathogens

Article Title: The HCMV gH/gL/UL128-131 Complex Triggers the Specific Cellular Activation Required for Efficient Viral Internalization into Target Monocytes

doi: 10.1371/journal.ppat.1003463

Figure Lengend Snippet: Integrin engagement and activation of the integrin/Src/paxillin signaling pathway by the gH/gL/UL128-131 complex allows efficient HCMV internalization into target monocytes. (A and B) Monocytes were pretreated with 1 µM PP2, 1 µM AG1478, 5 µg/ml of blocking anti-β1 or anti-β3 integrin antibodies, or 5 µg/ml of IgG for 1 h at 37°C/5% CO 2 . (C and D) Monocytes were transfected with siRNA complementary to paxillin or a control siRNA for 48 h. (A, B, C, and D) Monocytes were then HCMV (BADwt or BADrUL131)-infected (M.O.I. of 0.1) for 1 h at 4°C, washed, treated with 5 U/ml of α-thrombin (D only), then temperature shifted to 37°C for 1 h. Monocytes were washed and treated with Proteinase K solution for 1 h. Monocytes were then harvested and quantitative real-time PCR was performed using primers complementary to genomic HCMV DNA and 18S rRNA, as an internal control. Results are plotted as a mean ±SEM. Student's T-tests were performed and p

Article Snippet: Briefly, monocytes, fibroblasts, or epithelial cells were treated and then HCMV infected (M.O.I. of 0.1) for 1 h at 4°C, washed with 1× PBS (Mediatech, Inc.) and temperature shifted to 37°C for 1 h. Cells were washed and treated with 2 mg/ml solution of Proteinase K (Promega) for 1 h at 4°C.

Techniques: Activation Assay, Blocking Assay, Transfection, Infection, Real-time Polymerase Chain Reaction

Journal: PLoS Pathogens

Article Title: The HCMV gH/gL/UL128-131 Complex Triggers the Specific Cellular Activation Required for Efficient Viral Internalization into Target Monocytes

doi: 10.1371/journal.ppat.1003463

Figure Lengend Snippet: Presence of the gH/gL/UL128-131 complex links HCMV′s ability to activate and efficiently enter into target monocytes. (A) Approximately 2×10 6 virions of Towne (p.40, p.51 and p.57), AD169, TB40/E and TB40/F were spun down through a sucrose cushion, lysed and western blot analyses were performed using antibodies recognizing the HCMV proteins, pp65 and pUL130. (B) Monocytes were isolated and cultured in low serum for 24 h at 37°C/5% CO 2 . Monocytes were then mock- or HCMV (Towne p.40, Towne p.57, TB40/E, TB40/F, AD169)-infected (M.O.I. of 5) and harvested at 15 min. pi. Western blot analyses were performed using antibodies specific for the phosphorylated and non-phosphorylated forms of Src and p70 S6 kinase. Actin was used as a loading control. The results were also measured by densitometry with relative numbers shown in the figure. (C) Monocytes were mock infected or HCMV (Towne p.40, Towne p.57, TB40/E, TB40/F, AD169) infected (M.O.I. of 0.1) for 1 h at 4°C, then temperature shifted to 37°C for 1 h. Monocytes were washed and treated with Proteinase K solution for 1 h. Monocytes were then harvested and semi-quantitative PCR was performed using primers complementary to genomic HCMV DNA and cellular GAPDH, as an internal control. PCR reactions were analyzed by agarose gel electrophoresis using ethidium bromide. (D, E, F, G, H, I and J) Monocytes were mock- or HCMV (TB40/E or AD169)-infected (M.O.I. of 5) for 1 h at 4°C, then 2 mM of DTSSP [3,3′-dithiobis (sulfosuccinimidylpropionate] was added at 4°C for additional 2 h. Cells were spun down and lysed. Antibodies recognizing β1, β3 integrins, HCMV gH or isotype control IgG were added overnight at 4°C to cellular lysates and then protein A/G Sepharose was added for 4 h at 4°C. Protein A/G Sepharose beads with bound protein complexes were spun down, washed with a lysis buffer and resuspended in sample buffer. Western blot analyses were performed using antibodies recognizing β1 and β3 integrins, as well as the HCMV gH and pUL130. Lysates from HCMV-infected monocytes were also analyzed for equal levels of β1, β3 integrins and actin in samples undergoing immunoprecipitation. All experiments were repeated at least three times and representative results are shown. Note: The arrows point to the band of interest. The asterisks mark non-specific bands. (K) The schematic diagram describes our cumulative data from the immunoprecipitation analysis; illustrating the interaction between the gH/gL/UL128-131 complex of TB40/E strain or gH/gL/(gO) complex of AD169 strain with cellular integrins.

Article Snippet: Briefly, monocytes, fibroblasts, or epithelial cells were treated and then HCMV infected (M.O.I. of 0.1) for 1 h at 4°C, washed with 1× PBS (Mediatech, Inc.) and temperature shifted to 37°C for 1 h. Cells were washed and treated with 2 mg/ml solution of Proteinase K (Promega) for 1 h at 4°C.

Techniques: Western Blot, Isolation, Cell Culture, Infection, Real-time Polymerase Chain Reaction, Polymerase Chain Reaction, Agarose Gel Electrophoresis, Lysis, Immunoprecipitation

Journal: PLoS Pathogens

Article Title: The HCMV gH/gL/UL128-131 Complex Triggers the Specific Cellular Activation Required for Efficient Viral Internalization into Target Monocytes

doi: 10.1371/journal.ppat.1003463

Figure Lengend Snippet: Presence of the gH/gL/UL128-131 complex has no effect on the integrin/Src/paxillin signaling pathway in and HCMV internalization into fibroblasts. (A) Fibroblasts were cultured in low serum for 24 h at 37°C/5% CO 2 . Fibroblasts were then mock- or HCMV (BADwt or BADrUL131)-infected (M.O.I. of 5) and harvested at 20 min. pi. Western blot analyses were performed using antibodies specific for the phosphorylated and non-phosphorylated forms of Src, paxillin, and Erk. Actin was used as a loading control. The results were also measured by densitometry with relative numbers shown in the figure. (B) Fibroblasts were infected with BADwt or BADrUL131 (M.O.I. of 0.1) for 1 h at 4°C, then left at 4°C or temperature shifted to 37°C for 1 h. (C) Fibroblasts were transfected with siRNA complementary to paxillin or a control siRNA for 48 h. Fibroblasts were infected with BADwt or BADrUL131 (M.O.I. of 0.1) for 1 h at 4°C, then temperature shifted to 37°C for 1 h. (B and C) Then, fibroblasts were washed and treated with Proteinase K solution for 1 h. Cells were then harvested and quantitative real-time PCR was performed using primers complementary to genomic HCMV DNA and 18S rRNA, as an internal control. Results are plotted as a mean ±SEM. Student's T-tests were performed and p

Article Snippet: Briefly, monocytes, fibroblasts, or epithelial cells were treated and then HCMV infected (M.O.I. of 0.1) for 1 h at 4°C, washed with 1× PBS (Mediatech, Inc.) and temperature shifted to 37°C for 1 h. Cells were washed and treated with 2 mg/ml solution of Proteinase K (Promega) for 1 h at 4°C.

Techniques: Cell Culture, Infection, Western Blot, Transfection, Real-time Polymerase Chain Reaction

Journal: PLoS Pathogens

Article Title: The HCMV gH/gL/UL128-131 Complex Triggers the Specific Cellular Activation Required for Efficient Viral Internalization into Target Monocytes

doi: 10.1371/journal.ppat.1003463

Figure Lengend Snippet: Regulation of the actin cytoskeleton and dynamin is essential for efficient internalization of clinical-like HCMV isolates into monocytes, but not into fibroblasts. (A) Monocytes were pretreated with DMSO, 0.5 µM jasplakinolide, or 2.5 µM latrunculin A. (B) Monocytes were transfected with siRNA complementary to paxillin or a control siRNA for 48 h. (C) Monocytes were preatreated with 50 µM dynasore. (D) Monocytes were transfected with siRNA complementary to dynamin or a control siRNA for 48 h. (E and F) Fibroblasts were pretreated with DMSO, 0.5 µM jasplakinolide, 2.5 µM latrunculin A, or 50 µM dynasore. (A, B, C, D, E, and F) Cells were then infected with BADwt, BADrUL131 or TB40/E (M.O.I. of 0.1) for 1 h at 4°C washed and then temperature shifted to 37°C for 1 h. Monocytes were then treated with 0.5 µM jasplakinolide at 37°C for an additional 1 h (only B). Cells were then washed and treated with Proteinase K solution for 1 h. Cells were harvested and PCR was performed using primers complementary to genomic HCMV DNA and 18S rRNA. For qPCR data, results are plotted as a mean ±SEM. Student's T-tests were performed and p

Article Snippet: Briefly, monocytes, fibroblasts, or epithelial cells were treated and then HCMV infected (M.O.I. of 0.1) for 1 h at 4°C, washed with 1× PBS (Mediatech, Inc.) and temperature shifted to 37°C for 1 h. Cells were washed and treated with 2 mg/ml solution of Proteinase K (Promega) for 1 h at 4°C.

Techniques: Transfection, Infection, Polymerase Chain Reaction, Real-time Polymerase Chain Reaction

Journal: PLoS Pathogens

Article Title: The HCMV gH/gL/UL128-131 Complex Triggers the Specific Cellular Activation Required for Efficient Viral Internalization into Target Monocytes

doi: 10.1371/journal.ppat.1003463

Figure Lengend Snippet: The HCMV gH/gL/UL128-131 complex is critical for activation of, and for efficient and productive viral internalization into target monocytes. (A) Monocytes were cultured in low serum for 24 h at 37°C/5% CO 2 . Monocytes were then mock- or HCMV (BAD wt or BAD r UL131)-infected (M.O.I. of 5) and harvested at 15 min. pi. Western blot analyses were performed using antibodies specific for the phosphorylated and non-phosphorylated forms of Src, paxillin, Erk and SAPK/JNK. Actin was used as a loading control. The results were also measured by densitometry with relative numbers shown in the figure. (B) Monocytes were HCMV (BADwt, BADrUL131, TB40/F or TB40/E)-infected (M.O.I. of 0.1) for 1 h at 4°C, then temperature shifted to 37°C for 1 h. Monocytes were washed and treated with Proteinase K solution for 1 h. Monocytes were then harvested and quantitative real-time PCR was performed using primers complementary to genomic HCMV DNA and 18S rRNA, as an internal control. Results are plotted as a mean ±SEM. Student's T-tests were performed and p

Article Snippet: Briefly, monocytes, fibroblasts, or epithelial cells were treated and then HCMV infected (M.O.I. of 0.1) for 1 h at 4°C, washed with 1× PBS (Mediatech, Inc.) and temperature shifted to 37°C for 1 h. Cells were washed and treated with 2 mg/ml solution of Proteinase K (Promega) for 1 h at 4°C.

Techniques: Activation Assay, Cell Culture, Infection, Western Blot, Real-time Polymerase Chain Reaction

Journal: Frontiers in Microbiology

Article Title: Novel Multidrug-Resistant Enterococcal Mobile Linear Plasmid pELF1 Encoding vanA and vanM Gene Clusters From a Japanese Vancomycin-Resistant Enterococci Isolate

doi: 10.3389/fmicb.2019.02568

Figure Lengend Snippet: Retardation assay of pELF1 DNAs excised from PFGE or SDS-PFGE gels. DNA bands of pELF1 were excised from PFGE gel (proteinase K treatment +) or SDS-PFGE gel (proteinase K treatment –), and digested with Sac I (lanes 3 and 4), and Sma I (lanes 5 and 6). After digestion, the samples were subjected to PFGE. MM, Low Range PFG Marker; 1, pELF1 excised from PFGE gel; 2, pELF1 excised from SDS-PFGE gel; 3, Sac I-treated pELF1 excised from PFGE gel; 4, Sac I-treated pELF1 excised from SDS-PFGE gel; 5, Sma I-treated pELF1 excised from PFGE gel; 6, Sma I-treated pELF1 excised from SDS-PFGE gel. N. D.; not digested.

Article Snippet: Agarose plugs (1%) containing embedded enterococci were treated with lysozyme (Roche Diagnostics K.K, Minneapolis, MN, United States) solution (10 mg/ml) at 37°C for 6 h, followed by treatment with proteinase K (Merck Millipore, Darmstadt, Germany) solution (60 mAnson U/ml) at 50°C for 48 h. After washing the plugs with wash buffer (20 mM Tris-HCl, pH 8.0; 50 mM EDTA), proteinase K was inhibited using phenylmethylsulfonyl fluoride (PMSF) solution (20 mM Tris-HCl, pH 8.0, 50 mM EDTA, and 1 mM PMSF).

Techniques: Marker

Journal: Frontiers in Microbiology

Article Title: Novel Multidrug-Resistant Enterococcal Mobile Linear Plasmid pELF1 Encoding vanA and vanM Gene Clusters From a Japanese Vancomycin-Resistant Enterococci Isolate

doi: 10.3389/fmicb.2019.02568

Figure Lengend Snippet: PFGE of the restriction fragments of pELF1 with proteinase K treatment. Lanes: Low Range PFG Marker; proteinase K-treatment only; proteinase K-treated Sal I digests; proteinase K-treated Sma I digests; proteinase K-treated Eag I digests. N. D., not digested.

Article Snippet: Agarose plugs (1%) containing embedded enterococci were treated with lysozyme (Roche Diagnostics K.K, Minneapolis, MN, United States) solution (10 mg/ml) at 37°C for 6 h, followed by treatment with proteinase K (Merck Millipore, Darmstadt, Germany) solution (60 mAnson U/ml) at 50°C for 48 h. After washing the plugs with wash buffer (20 mM Tris-HCl, pH 8.0; 50 mM EDTA), proteinase K was inhibited using phenylmethylsulfonyl fluoride (PMSF) solution (20 mM Tris-HCl, pH 8.0, 50 mM EDTA, and 1 mM PMSF).

Techniques: Marker

Journal: Frontiers in Microbiology

Article Title: Novel Multidrug-Resistant Enterococcal Mobile Linear Plasmid pELF1 Encoding vanA and vanM Gene Clusters From a Japanese Vancomycin-Resistant Enterococci Isolate

doi: 10.3389/fmicb.2019.02568

Figure Lengend Snippet: PFGE of the AA708 strain. Lanes: Low Range PFG Marker; AA708 without proteinase K treatment; AA708 with proteinase K treatment; AA708 with both proteinase K and S1 nuclease treatment.

Article Snippet: Agarose plugs (1%) containing embedded enterococci were treated with lysozyme (Roche Diagnostics K.K, Minneapolis, MN, United States) solution (10 mg/ml) at 37°C for 6 h, followed by treatment with proteinase K (Merck Millipore, Darmstadt, Germany) solution (60 mAnson U/ml) at 50°C for 48 h. After washing the plugs with wash buffer (20 mM Tris-HCl, pH 8.0; 50 mM EDTA), proteinase K was inhibited using phenylmethylsulfonyl fluoride (PMSF) solution (20 mM Tris-HCl, pH 8.0, 50 mM EDTA, and 1 mM PMSF).

Techniques: Marker

Journal: Frontiers in Microbiology

Article Title: Novel Multidrug-Resistant Enterococcal Mobile Linear Plasmid pELF1 Encoding vanA and vanM Gene Clusters From a Japanese Vancomycin-Resistant Enterococci Isolate

doi: 10.3389/fmicb.2019.02568

Figure Lengend Snippet: SDS-PFGE of the AA708 strain. Lanes: Low Range PFG Marker; AA708 with proteinase K treatment; AA708 without proteinase K treatment; AA708 with proteinase K and S1 nuclease treatment.

Article Snippet: Agarose plugs (1%) containing embedded enterococci were treated with lysozyme (Roche Diagnostics K.K, Minneapolis, MN, United States) solution (10 mg/ml) at 37°C for 6 h, followed by treatment with proteinase K (Merck Millipore, Darmstadt, Germany) solution (60 mAnson U/ml) at 50°C for 48 h. After washing the plugs with wash buffer (20 mM Tris-HCl, pH 8.0; 50 mM EDTA), proteinase K was inhibited using phenylmethylsulfonyl fluoride (PMSF) solution (20 mM Tris-HCl, pH 8.0, 50 mM EDTA, and 1 mM PMSF).

Techniques: Marker

Journal: BMC Research Notes

Article Title: Proteinase K treatment improves RNA recovery from thyroid cells fixed with liquid-based cytology solution

doi: 10.1186/s13104-018-3914-4

Figure Lengend Snippet: The effect of Proteinase K treatment on RNA recovery from CytoRichRed-fixed K1 cells. RNA was extracted from filter-trapped K1 cells after incubation with Proteinase K-containing and Proteinase K-free buffers for 3 h at 55 °C

Article Snippet: The filters with the trapped cells were washed with PBS and incubated in 500 μl lysis buffer [10 mM Tris–HCl (pH 7.8), 5 mM EDTA and 0.5% SDS] with or without 400 mg/ml Proteinase K (Wako) at 55 °C.

Techniques: Incubation

Journal: BMC Research Notes

Article Title: Proteinase K treatment improves RNA recovery from thyroid cells fixed with liquid-based cytology solution

doi: 10.1186/s13104-018-3914-4

Figure Lengend Snippet: Effect of Proteinase K treatment on RNA recovery from CytoRichRed-fixed thyroid FNAB specimens. The thyroid FNAB specimens processed for LBC using CytoRich-Red solution were trapped to filters in the same way as described above. RNA was extracted from the specimens after incubation with Proteinase K-containing and Proteinase K-free buffers for 3 h at 55 °C

Article Snippet: The filters with the trapped cells were washed with PBS and incubated in 500 μl lysis buffer [10 mM Tris–HCl (pH 7.8), 5 mM EDTA and 0.5% SDS] with or without 400 mg/ml Proteinase K (Wako) at 55 °C.

Techniques: Incubation

Journal: BMC Research Notes

Article Title: Proteinase K treatment improves RNA recovery from thyroid cells fixed with liquid-based cytology solution

doi: 10.1186/s13104-018-3914-4

Figure Lengend Snippet: RNA recovery from filter-trapped K1 cells fixed for liquid-based cytology. RNA was extracted from the fixed K1 cells after incubation with Proteinase K-containing for the indicated periods at 55 °C. RNA recovery from K1 cells fixed with CytoRich-Red ( a ) and CytoRich-Blue ( b ). Black bars and gray bars represent the RNA yield from 20,000 to 100,000 cells, respectively. Quality of RNAs extracted from K1 cells fixed with CytoRich-Red ( c ) and CytoRich-Blue ( d ). The analysis using Agilent 2100 bioanalyzer revealed that 28S and 18S ribosomal RNAs (correspond to the bands at approximately 1900 nt and 3900 nt on the charts, respectively) remained nearly intact, leading to high RINs. N/A not assessed

Article Snippet: The filters with the trapped cells were washed with PBS and incubated in 500 μl lysis buffer [10 mM Tris–HCl (pH 7.8), 5 mM EDTA and 0.5% SDS] with or without 400 mg/ml Proteinase K (Wako) at 55 °C.

Techniques: Incubation

Journal: Veterinary Sciences

Article Title: Characterization of Ethanol Extracted Cell Wall Components of Mycobacterium avium Subsp. paratuberculosis

doi: 10.3390/vetsci6040088

Figure Lengend Snippet: Preparation of EtOH extract for mass spectrometry analysis. ( a ) Map bacilli were washed 6 times prior to EtOH extraction (labeled × 6) to avoid bovine serum albumin (BSA) contamination. A second extract was prepared after washing Map once (label × 1). Lipids and carbohydrate were removed from the EtOH extract through a second chloroform:methanol:water extraction. This second extraction was run on 12% SDS-PAGE denaturing gels and exposed to Coomassie stain (CBB) and silver stain. The location of BSA migration is identified for both gel images. ( b ) Proteinase K treatment of Map EtOH extract. Inclusion of proteinase K or the EtOH extract along with staining method is indicated beneath the gel. Kilodalton size markers are shown in the left margins of all gels.

Article Snippet: In the ELISA experiment, to measure antibody binding, proteinase K (200 µg/mL; ACROS Organics-Thermo Fisher Scientific, Pittsburgh, PA, USA) was used.

Techniques: Mass Spectrometry, Labeling, SDS Page, Staining, Silver Staining, Migration

Journal: Veterinary Sciences

Article Title: Characterization of Ethanol Extracted Cell Wall Components of Mycobacterium avium Subsp. paratuberculosis

doi: 10.3390/vetsci6040088

Figure Lengend Snippet: Bovine antibody binds to a carbohydrate component of the Map EtOH extract, not to protein. ( a ) Surface antigens of Map K-10 were extracted with 80% ethanol (EtOH Whole) and fractionated by Folch extraction method into organic (chloroform), interface and aqueous fractions. After evaporating methanol for immobilization of the lipids (and other molecules) onto the wells of a microtitre plate, they were incubated with serum samples (1:100 dilution) collected from JD-positive (solid bar) and negative (open bar) cattle. Histogram bars represent mean antibody binding ± standard deviation of quadruplicate determinations. Most of the antigenicity is in the organic fraction. ( b ) EtOH extract treated with proteases shows no negative effects on bovine antibody binding. The extract was treated with either 10 µg/mL trypsin or 10 µg/mL proteinase K with each treatment actually enhancing antibody binding. This enhancement was not statistically significant. However, EtOH extract antigens are efficiently removed by ConA-agarose as shown by lack of antibody binding ( c ). Absorption with agarose only does not affect antibody binding to the EtOH extract. This experiment was repeated in triplicate with qraduplicate measurements for each. p values less than 0.01 are denoted by an asterisk.

Article Snippet: In the ELISA experiment, to measure antibody binding, proteinase K (200 µg/mL; ACROS Organics-Thermo Fisher Scientific, Pittsburgh, PA, USA) was used.

Techniques: Incubation, Binding Assay, Standard Deviation

Journal: PLoS ONE

Article Title: Degradation of RNA during lysis of Escherichia coli cells in agarose plugs breaks the chromosome

doi: 10.1371/journal.pone.0190177

Figure Lengend Snippet: Characterization of RiCF. (A) Representative radiogram showing RNase dose dependent chromosomal fragmentation in AB1157. Plugs were made with 0, 2, 10, 25, 50 or 100 μg RNase and lysed and electrophoresed under standard conditions. CZ, compression zone. (B) Quantification showing increase in chromosomal fragmentation in RNase dose-dependent manner. Data points are means of six independent assays ± SEM. (C) RNase-effect is not seen in the pre-lyzed cells. Plugs from AB1157 culture were made in the presence of proteinase K, but without any RNase. After overnight lysis and extensive washing, the plugs were incubated with 0, 2, 20 and 100 μg RNase or 100 U of EcoRI for 15 H at 37°C before PFGE. (D) Quantification of chromosomal fragmentation showing extreme sensitivity of chromosomes to EcoRI, but not RNase, when plugs were treated with the enzymes after lysis of cells. The experiment is done twice and a representative result is presented. (E) A representative radiogram showing kinetics of RiCF. Multiple plugs were made in the presence of RNase (50 μg/plug) and incubated at 62°C for 10, 30, 60, 180 or 900 minutes with lysis buffer in individual tubes. At the indicated times, one tube was removed, lysis buffer was replaced with ice-cold TE, and plugs were stored at 4°C until all plugs were ready for electrophoresis. (F) Quantification of kinetics of chromosomal fragmentation when plugs were made in the presence of RNase and lysed for 1, 5, 10, 30, 60, 180 or 900 minutes. Data points are means of three independent assays ± SEM. Arrow shows the value of fragmentation after 10 min lysis.

Article Snippet: To make agarose plugs, 5 μl of proteinase K (from 5 mg/ml stock) and 65 μl of molten and cooled to 75°C agarose (either plain or lysis-plug agarose) was added to the cell suspension, and the mixture was quickly transferred to plug molds (Bio-Rad).

Techniques: Lysis, Incubation, Electrophoresis

Journal: PLoS ONE

Article Title: Degradation of RNA during lysis of Escherichia coli cells in agarose plugs breaks the chromosome

doi: 10.1371/journal.pone.0190177

Figure Lengend Snippet: Genetics of RiCF. (A) Quantitative determination of RiCF in Δ hns mutant. AB1157 and SRK254 were grown at 37°C to the same final OD, and plugs were made in the absence of proteinase K, but with or without RNase (50 μg/plug). After overnight incubation in the lysis buffer at 62°C, the plugs were electrophoresed under standard conditions. Data points are means of 6–10 independent assays± SEM. (B) Radiogram of a representative pulsed field gel from which data in (A) are calculated. (C) Comparison of RiCF in Δ hupA Δ hupB and Δ ihfA Δ ihfB double mutants. Experiment was done as described in (A), and values presented are means of 6–13 independent assays ± SEM. (D) Radiogram of a representative pulsed field gel from which data in (C) are calculated. (E) Effect of hns deletion on RiCF of Δ ihfA Δ ihfB mutant. Values presented are means of 7 independent assays ± SEM.

Article Snippet: To make agarose plugs, 5 μl of proteinase K (from 5 mg/ml stock) and 65 μl of molten and cooled to 75°C agarose (either plain or lysis-plug agarose) was added to the cell suspension, and the mixture was quickly transferred to plug molds (Bio-Rad).

Techniques: Mutagenesis, Incubation, Lysis, Pulsed-Field Gel

Journal: PLoS ONE

Article Title: Degradation of RNA during lysis of Escherichia coli cells in agarose plugs breaks the chromosome

doi: 10.1371/journal.pone.0190177

Figure Lengend Snippet: Non-coding RNA and HU stabilize nucleoids. (A) Comparison of spontaneous and RNase-induced fragmentation in Δ nc1 Δ nc5 Δ ihfA Δ ihfB , Δ nc1 Δ nc5 Δ hupA Δ hupB and Δ nc1 Δ nc5 Δ hns mutants. AB1157, SRK254-12, SRK254-15 and SRK254-18 were grown at 37°C, and plugs were made in absence of proteinase K, both with or without RNase (50 μg/plug), and lysed under standard conditions. Data points are means of at least three independent assays± SEM. (B) Radiogram of a representative gel from which data in (A) are generated.

Article Snippet: To make agarose plugs, 5 μl of proteinase K (from 5 mg/ml stock) and 65 μl of molten and cooled to 75°C agarose (either plain or lysis-plug agarose) was added to the cell suspension, and the mixture was quickly transferred to plug molds (Bio-Rad).

Techniques: Generated

Journal: PLoS ONE

Article Title: Degradation of RNA during lysis of Escherichia coli cells in agarose plugs breaks the chromosome

doi: 10.1371/journal.pone.0190177

Figure Lengend Snippet: Endonuclease-I is critical for RiCF but not for spontaneous fragmentation. (A) Comparison of spontaneous fragmentation and RiCF in AB1157, AB1157 Δ nc1 Δ nc5 Δ hupA Δ hupB and AB1157 Δ nc1 Δ nc5 Δ hupA Δ hupB Δ endA mutants. All strains were grown at 37°C to the final OD of 0.6, and plugs were made in the absence of proteinase K, both with or without RNase (50 μg/plug). Data points are means of at least three independent assays ± SEM. (B) Radiogram of a representative gel from which data in (A) are generated.

Article Snippet: To make agarose plugs, 5 μl of proteinase K (from 5 mg/ml stock) and 65 μl of molten and cooled to 75°C agarose (either plain or lysis-plug agarose) was added to the cell suspension, and the mixture was quickly transferred to plug molds (Bio-Rad).

Techniques: Generated

Journal: PLoS ONE

Article Title: Degradation of RNA during lysis of Escherichia coli cells in agarose plugs breaks the chromosome

doi: 10.1371/journal.pone.0190177

Figure Lengend Snippet: RNA degradation causes chromosomal fragmentation. (A) Schematics of a hypothetical scenario when RNA makes the central core of nucleoids, and its degradation results in collapse of the nucleoid structure, causing chromosomal fragmentation. (B) Radiogram of a pulsed field gel showing chromosomal fragmentation in AB1157 when cells were embedded in agarose plugs in the presence and absence of proteinase K (25 μg/plug) and/or RNase (50 μg/plug) and lysed overnight at 62°C. (C) Radiogram showing DNase I sensitivity of the signal entering the gel. Plugs were lysed at 62°C, washed extensively to remove traces of lysis buffer and then treated with DNase I at 37°C before PFGE. (D) A representative gel showing that RNA degradation by different enzymes causes chromosomal fragmentation. Plugs were made in the absence of proteinase K in 1x restriction enzyme buffer (NEBuffer 3 for RNase A, XRN-1 and RNAse I f and NEBuffer 4 for Exo T). The concentrations of the enzymes used were, RNase, 50 μg/plug; XRN-1, 5 U/plug; RNAse I f , 100 U/plug and Exo T, 20 U/plug. (E) Quantification of the chromosomal fragmentation when plugs were made in the presence of various RNA degrading enzymes. The values presented are means of four independent assays ± SEM. CZ, compression zone.

Article Snippet: To make agarose plugs, 5 μl of proteinase K (from 5 mg/ml stock) and 65 μl of molten and cooled to 75°C agarose (either plain or lysis-plug agarose) was added to the cell suspension, and the mixture was quickly transferred to plug molds (Bio-Rad).

Techniques: Pulsed-Field Gel, Lysis

Journal: Nucleic Acids Research

Article Title: Linear Streptomyces plasmids form superhelical circles through interactions between their terminal proteins

doi: 10.1093/nar/gkq1204

Figure Lengend Snippet: In vivo cross-linking of telomeres. Mycelium from liquid cultures was treated with DSS or DSG. Total DNA was isolated, digested with BclI (Bc) or BglII (Bg), fractionated by gel electrophoresis and hybridized to labeled plasmid DNA. ( A ) pLUS891L. The physical map of the plasmid DNA is shown above. The sizes of the restriction fragments are indicated (in kb). tsr , thiostrepton resistance gene; ARS, autonomously replicating sequence of pSLA2; filled arrows, SCP1 telomeres; filled circles, Tpc proteins. The DNA linked by the cross-linker is indicated by an asterisk. ‘M’, DNA size markers. The size of the DNA fragments is depicted on the left (in kb). A set of samples was treated with proteinase K (‘+’) before electrophoresis (right panel). ( B ) pLUS892L. The symbols and analyses are as in (A).

Article Snippet: To remove TP, proteinase K (AMRESCO) was added to the loading buffer containing the DNA sample to a final concentration of 20 U/ml before electrophoresis.

Techniques: In Vivo, Isolation, Nucleic Acid Electrophoresis, Labeling, Plasmid Preparation, Sequencing, Electrophoresis

Journal: Nucleic Acids Research

Article Title: Linear Streptomyces plasmids form superhelical circles through interactions between their terminal proteins

doi: 10.1093/nar/gkq1204

Figure Lengend Snippet: In vitro cross-linking of telomeres. ( A ) Without GnHCl treatment. Total DNA of S. lividans 3200/pLUS891L was treated with DSS or DSG, digested with BclI (Bc) or BglII (Bg), fractionated by gel electrophoresis and hybridized with pLUS891L DNA probe. ( B ) With GnHCl treatment. Genomic DNA of S. lividans 3200/pLUS892L was isolated by GnHCl–CsCl gradient centrifugation and treated with DSS or DSG. The treated DNA was digested with BclI or MluI, fractionated by gel electrophoresis and hybridized to the SCP1 terminal DNA probe. The physical map of pLUS892L is shown above with the BclI and MluI (Ml) sites and fragments sizes indicated. In the control experiment (right panel), the samples were treated with proteinase K before electrophoresis. The cross-linked DNA is indicated by an asterisk.

Article Snippet: To remove TP, proteinase K (AMRESCO) was added to the loading buffer containing the DNA sample to a final concentration of 20 U/ml before electrophoresis.

Techniques: In Vitro, Nucleic Acid Electrophoresis, Isolation, Gradient Centrifugation, Electrophoresis

Journal: Nucleic Acids Research

Article Title: Linear Streptomyces plasmids form superhelical circles through interactions between their terminal proteins

doi: 10.1093/nar/gkq1204

Figure Lengend Snippet: Superhelical structures formed by linear plasmid DNA. ( A ) S. lividans 3200/pLUS892L mycelium was osmotically lysed. The cell lysate was treated with E. coli Topoisomerase I (‘Topo I’), fractionated by gel electrophoresis and hybridized to the pLUS892L DNA probe. In the control experiments, samples were treated with proteinase K (‘PK’) before electrophoresis, or the topoisomerase treatment was omitted, or both. The sizes of the (proteinase K-treated) linear pLUS892L DNA and the marker DNAs (‘M’) are indicated (in kb). ( B ) AFM examination of isolated DSS-cross-linked linear plasmid DNA (pLUS891L) without proteinase K-treatment (‘−PK’) shows supercoiled DNA structures that are held together by telomere–telomere interactions (left and center images). The center image shows a zoomed-in surface plot of the coiled DNA molecule boxed in the left image. Proteolytic digestion of the DSS-cross-linked DNA by proteinase K (‘+PK’) transformed it into relaxed, linear structures (right). The scale bar is 1 µm.

Article Snippet: To remove TP, proteinase K (AMRESCO) was added to the loading buffer containing the DNA sample to a final concentration of 20 U/ml before electrophoresis.

Techniques: Plasmid Preparation, Nucleic Acid Electrophoresis, Electrophoresis, Marker, Isolation, Transformation Assay

Journal: Nature Communications

Article Title: Self-replication of DNA by its encoded proteins in liposome-based synthetic cells

doi: 10.1038/s41467-018-03926-1

Figure Lengend Snippet: Potentiating DNA self-replication with 5′-end pre-bound TP. a IVTTR reaction scheme using the TP- oriLR-p2-p3 DNA template. Short amplification products are not represented. The detailed experimental workflow, including preparation of the TP- oriLR-p2-p3 DNA, is shown in Supplementary Fig. 12a . b The replication products of the TP- oriLR-p2-p3 DNA template (∼75 ng input, equiv. ∼1.9 nM) expressed in PURE frex were visualized on agarose gel after RNase and Proteinase K treatments, followed by RNeasy clean-up column purification. When indicated the p6-p5 DNA (70 ng input, equiv. ∼5.7 nM) was co-expressed. The results from two independent IVTTR experiments are shown in Supplementary Fig. 12c, f . For direct comparison of the amplification yield with and without parental TP, similar amounts of input DNA were used, the end-point reaction solutions were loaded on the same gel and the band intensities were analysed (Supplementary Fig. 13 ). Clearly, replication of the TP- oriLR-p2-p3 DNA template is more efficient. c Samples were further incubated with λ-exonuclease to remove TP-uncapped DNA. Note that the overall amount of DNA on the gel is reduced (to the extent that the band corresponding to the input TP- oriLR-p2-p3 DNA in the –dNTPs control sample is no longer visible) after nuclease treatment due to dilution during the cleaning/purification steps. d De novo synthesized DNA was subsequently used as a template for a third IVTT reaction. The translation products were visualized by PAGE with GreenLys labeling. The protein gel analysis from an independent IVTTR experiment is shown in Supplementary Fig. 12d . e Autocatalytic IVTTR cycles realized in this study. A first IVTTR reaction was performed using oriLR-p2-p3 as input DNA and producing larger amount of TP- oriLR-p2-p3 (Supplementary Fig. 12b, e ). The purified TP- oriLR-p2-p3 DNA was subsequently used as template for a second IVTTR ( b ). Finally, the purified DNA products from IVTTR 2 was used for a third IVTT ( d )

Article Snippet: Using a cut tip to prevent liposome breakage, 2 μL of the liposome solution was added to 5.5 μL of feeding solution, consisting of milli-Q, PUREfrex Solution I (v/v 7:4) and 91 μg/mL proteinase K. The diluted liposome mixture was incubated overnight at 30 °C in an Eppendorf tube.

Techniques: Amplification, Agarose Gel Electrophoresis, Purification, Incubation, Synthesized, Polyacrylamide Gel Electrophoresis, Labeling

Journal: Nature Communications

Article Title: Self-replication of DNA by its encoded proteins in liposome-based synthetic cells

doi: 10.1038/s41467-018-03926-1

Figure Lengend Snippet: Replication of DNA by its encoded proteins. a IVTTR reaction scheme using the oriLR-p2-p3 DNA template. Short amplification products are not represented. b The replication products of either the oriLR-p2-p3 or the p2-p3 DNA template (100 ng input) expressed in PURE frex were visualized on agarose gel after RNase and Proteinase K treatments, followed by RNeasy clean-up column purification. The results from five independent replication experiments are shown in Supplementary Fig. 9a , Supplementary Fig. 10 and Supplementary Fig. 12b,e . In each IVTTR reaction triggered by the expression of the oriLR-p2-p3 DNA construct, 2.5 nM of template produced about 100 nM of p2 and 700 nM of p3 proteins (as estimated in Supplementary Fig. 3 ), which were able to generate ~50 nM of full-length DNA product when the reaction was supplemented with purified p5 and p6. c Samples were further incubated with λ-exonuclease to remove TP-uncapped DNA. The asterisk indicates full-length TP-capped DNA that has not been degraded by the λ-exonuclease. d De novo synthesized DNA was subsequently used as a template for a second IVTT reaction. The translation products were visualized by PAGE with GreenLys labeling. Expression of DNA that resulted from an IVTTR in the presence of purified p5 and p6 proteins led to fluorescent p2 and p3 protein bands of similar intensity as that measured when starting with 2.5 nM purified DNA (control with PCR product) demonstrating that the encoded functions are retained during amplification. Protein gels from two independent replication experiments are shown in Supplementary Fig. 9b and Supplementary Fig. 11 . Note that the modest replication efficiency in the absence of purified p5 and p6 was sufficient to generate the encoded p2 and p3 proteins through amplification of information at the transcription and, to a lower extent, at the translation levels

Article Snippet: Using a cut tip to prevent liposome breakage, 2 μL of the liposome solution was added to 5.5 μL of feeding solution, consisting of milli-Q, PUREfrex Solution I (v/v 7:4) and 91 μg/mL proteinase K. The diluted liposome mixture was incubated overnight at 30 °C in an Eppendorf tube.

Techniques: Amplification, Agarose Gel Electrophoresis, Purification, Expressing, Construct, Produced, Incubation, Synthesized, Polyacrylamide Gel Electrophoresis, Labeling, Polymerase Chain Reaction

Journal: bioRxiv

Article Title: Quantitative proteomics links the LRRC59 interactome to mRNA translation on the ER membrane

doi: 10.1101/2020.03.04.975474

Figure Lengend Snippet: BioID-SEC62 labels functionally diverse proteins. (A) Comparison of protein abundance for the 353 identified putative interactors in SEC62-BirA and empty vector control HEK293 cells. Orange dots represent enriched, high-confidence proteins that interact with SEC62-BirA. Gray dots represent proteins that are less likely bona fide interactors of SEC62-BirA. (B) Hierarchical view of relationships for GO terms associated with SEC62 high-confidence protein interactors. GO term circles are outlined to match the colors assigned to each enriched GO category, as indicated beneath the panel. Circle sizes represent the number of genes in each enriched term, whereas circle color indicates the GO enrichment p -value. (C) Clustering of SEC62 high-confidence interactors based on co-occurrence of functional annotations. The left-most heatmap represents protein abundance values across biological replicates in control and SEC62-BirA HEK293 cells. (D) Protein-protein interactions (PPI) among high-confidence SEC62-BirA interactors, based on STRING annotations. Proteins are color-coded to match their functional assignment, as indicated above the panel. (E) Topology analysis of SEC62-BirA reporter line. SEC62-BirA cultures were chilled on ice, permeabilized with a digitonin-supplemented cytosol buffer, and subjected to digestion with the indicated concentrations of Proteinase K for 30 min on ice. Cells were subsequently lysed and total protein was resolved via SDS-PAGE (top panel). Following transfer, membranes were probed for GRP94 (ER-luminal protein), TRAP α (ER-resident protein with cytosolically-disposed antibody epitope), and BirA (BioID-SEC62 reporter). Lanes 1, 2, and 3 represent digestions with 0, 25, and 50 μg/ml proteinase K, respectively.

Article Snippet: Cultures were then placed on ice, permeabilized in digitonin-supplemented cytosolic buffer (as described above), rinsed, and incubated with cytosolic buffer containing 0, 25, or 50 µg/mL of Proteinase K (Bioline) for 30 minutes at 4°C.

Techniques: Plasmid Preparation, Functional Assay, SDS Page